5DGF

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

Melnikov, S.Mailliot, J.Shin, B.-S.Rigger, L.Yusupova, G.Micura, R.Dever, T.E.Yusupov, M.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth S0], CC [auth s0]251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-AC [auth S1], DC [auth s1]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth S2], EC [auth s2]253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth S3], FC [auth s3]239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-AF [auth S4], GC [auth s4]260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5G [auth S5], HC [auth s5]224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-AH [auth S6], IC [auth s6]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-AI [auth S7], JC [auth s7]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8-AJ [auth S8], KC [auth s8]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-AK [auth S9], LC [auth s9]196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10-AL [auth C0], MC [auth c0]96Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-AM [auth C1], NC [auth c1]155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12N [auth C2], OC [auth c2]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13O [auth C3], PC [auth c3]150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-AP [auth C4], QC [auth c4]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15 (uS19)Q [auth C5], RC [auth c5]141Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-AR [auth C6], SC [auth c6]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-AS [auth C7], TC [auth c7]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-AT [auth C8], UC [auth c8]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-AU [auth C9], VC [auth c9]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20V [auth D0], WC [auth d0]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-AW [auth D1], XC [auth d1]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AX [auth D2], YC [auth d2]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-AY [auth D3], ZC [auth d3]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-AZ [auth D4], AD [auth d4]134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-AAA [auth D5], BD [auth d5]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-BBA [auth D6], CD [auth d6]97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-ACA [auth D7], DD [auth d7]81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-ADA [auth D8], ED [auth d8]66Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-AEA [auth D9], FD [auth d9]55Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-AFA [auth E0], GD [auth e0]62Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31GA [auth E1], HD [auth e1]76Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinHA [auth SR], ID [auth sR]318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor protein STM1IA [auth SM], JD [auth sM]273Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AMA [auth L2], ND [auth l2]253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3NA [auth L3], OD [auth l3]386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AOA [auth L4], PD [auth l4]361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5PA [auth L5], QD [auth l5]296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AQA [auth L6], RD [auth l6]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-ARA [auth L7], SD [auth l7]243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-ASA [auth L8], TD [auth l8]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9-ATA [auth L9], UD [auth l9]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10UA [auth M0], VD [auth m0]220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11-BVA [auth M1], WD [auth m1]173Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
UniProt
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13-AWA [auth M3], YD [auth m3]198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AXA [auth M4], ZD [auth m4]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AYA [auth M5], AE [auth m5]203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-AZA [auth M6], BE [auth m6]198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-AAB [auth M7], CE [auth m7]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-ABB [auth M8], DE [auth m8]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
UniProt
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-ACB [auth M9], EE [auth m9]188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-ADB [auth N0], FE [auth n0]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21-AEB [auth N1], GE [auth n1]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
UniProt
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-AFB [auth N2], HE [auth n2]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 59
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60S ribosomal protein L23-AGB [auth N3], IE [auth n3]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24-AHB [auth N4], JE [auth n4]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 61
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60S ribosomal protein L25IB [auth N5], KE [auth n5]141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-AJB [auth N6], LE [auth n6]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27-AKB [auth N7], ME [auth n7]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28LB [auth N8], NE [auth n8]148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 65
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60S ribosomal protein L29MB [auth N9], OE [auth n9]58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 66
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60S ribosomal protein L30NB [auth O0], PE [auth o0]104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 67
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60S ribosomal protein L31-AOB [auth O1], QE [auth o1]112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 68
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60S ribosomal protein L32PB [auth O2], RE [auth o2]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-AQB [auth O3], SE [auth o3]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 70
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60S ribosomal protein L34-ARB [auth O4], TE [auth o4]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-ASB [auth O5], UE [auth o5]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-ATB [auth O6], VE [auth o6]99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-AUB [auth O7], WE [auth o7]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38VB [auth O8], XE [auth o8]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39WB [auth O9], YE [auth o9]50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40XB [auth Q0], ZE [auth q0]52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-AYB [auth Q1], AF [auth q1]25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-AZB [auth Q2], BF [auth q2]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-AAC [auth Q3], CF [auth q3]91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L12-A (uL11)XD [auth m2]165Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0DF [auth p0]311Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein P1 alpha/P2 betaEF [auth p1], FF [auth p2]47Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A-1GF [auth f]157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HYP2TIF51AYEL034WSYGP-ORF21
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
CH-CH-8AN-PRO-PROHF [auth B], IF [auth C]5Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth 2], BC [auth 6]1800Saccharomyces cerevisiae S288C
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Entity ID: 36
MoleculeChainsLengthOrganismImage
25S ribosomal RNAJA [auth 1], KD [auth 5]3396Saccharomyces cerevisiae S288C
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Entity ID: 37
MoleculeChainsLengthOrganismImage
5S ribosomal RNAKA [auth 3], LD [auth 7]121Saccharomyces cerevisiae S288C
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Entity ID: 38
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNALA [auth 4], MD [auth 8]158Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPS (Subject of Investigation/LOI)
Query on SPS

Download Ideal Coordinates CCD File 
NF [auth 1], NG [auth B]SPARSOMYCIN
C13 H19 N3 O5 S2
XKLZIVIOZDNKEQ-CLQLPEFOSA-N
 Ligand Interaction
OHX (Subject of Investigation/LOI)
Query on OHX

Download Ideal Coordinates CCD File 
GG [auth 5], RF [auth 1], SF [auth 1]osmium (III) hexammine
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AG [auth e1] , HG [auth o7] , IG [auth q0] , JF [auth D6] , JG [auth q2] , KF [auth D7] , KG [auth q3] , LF [auth D9] , 
AG [auth e1],  HG [auth o7],  IG [auth q0],  JF [auth D6],  JG [auth q2],  KF [auth D7],  KG [auth q3],  LF [auth D9],  MF [auth E1],  TF [auth O7],  UF [auth Q0],  VF [auth Q2],  WF [auth Q3],  XF [auth d6],  YF [auth d7],  ZF [auth d9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BG [auth 5] , CG [auth 5] , DG [auth 5] , EG [auth 5] , FG [auth 5] , LG [auth f] , MG [auth f] , OF [auth 1] , 
BG [auth 5],  CG [auth 5],  DG [auth 5],  EG [auth 5],  FG [auth 5],  LG [auth f],  MG [auth f],  OF [auth 1],  OG [auth B],  PF [auth 1],  PG [auth C],  QF [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 435.58α = 90
b = 287.33β = 98.95
c = 303.82γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondation pour la Recherche MedicaleFrance--
French National Research AgencyFranceANR-11-BSV8-006 01
Austrian Science FundAustriaP21641
Austrian Science FundAustriaI1040
European Research Council294312
Human Frontier Science ProgramRGP0062
Human Frontier Science ProgramRGP2012
Russian Government Program of Competitive Growh of Kazan Federal UniversityRussian Federation--
Intramural Research Program of the National Institutes of HealthUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Structure summary
  • Version 1.2: 2017-08-30
    Changes: Advisory, Author supporting evidence, Derived calculations