8A98

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : snoRNA MUTANT

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : snoRNA MUTANT

Rajan, K.S.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15A [auth SW]152Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QBV0 (Leishmania major)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24B [auth SZ]137Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1D2 (Leishmania major)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S21C [auth SY]164Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QH01 (Leishmania major)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinD [auth SX]161Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AEE8 (Leishmania major)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S17E [auth SV]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q806 (Leishmania major)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S11F [auth SU]173Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S13G [auth ST]151Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q3M1 (Leishmania major)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S29H [auth SS]57Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q817 (Leishmania major)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S18I [auth SR]153Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1Y3 (Leishmania major)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAJ [auth SB]246Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q0Q0 (Leishmania major)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S3K [auth SC]219Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q4A0 (Leishmania major)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S9L [auth SD]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QIM3 (Leishmania major)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4M [auth SE]273Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG31 (Leishmania major)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8N [auth SK]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for P25204 (Leishmania major)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1P [auth Sg]312Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q7Y7 (Leishmania major)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25Q [auth Sa]120Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q9X4 (Leishmania major)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S27-1R [auth Sc]86Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q140 (Leishmania major)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30S [auth Se]66Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q7P0 (Leishmania major)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12U [auth SQ]141Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG97 (Leishmania major)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S23V [auth SP]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QC89 (Leishmania major)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14W [auth SO]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q8H1 (Leishmania major)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S10X [auth SN]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1X7 (Leishmania major)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S33Y [auth Sd]87Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q931 (Leishmania major)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S20Z [auth SM]116Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q8G4 (Leishmania major)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S16AA [auth SL]149Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q9A5 (Leishmania major)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15ABA [auth SJ]130Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QGW3 (Leishmania major)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7CA [auth SI]200Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AC32 (Leishmania major)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5DA [auth SH]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q868B1 (Leishmania major)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6EA [auth SG]249Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q9NE83 (Leishmania major)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2FA [auth SF]265Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aGA [auth SA]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4FX73 (Leishmania major)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26HA [auth Sb]112Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q8L6 (Leishmania major)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Putative RNA binding proteinIA [auth Sh]235Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32JA [auth f]133Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30KA [auth d]104Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L7LA [auth c]252Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L35MA [auth a]127Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29NA [auth b]70Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q178 (Leishmania major)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L3SA [auth B]419Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q2Q6 (Leishmania major)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L2VA [auth A]260Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4FWX5 (Leishmania major)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L5WA [auth O]305Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AF09 (Leishmania major)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aXA [auth G]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QIP1 (Leishmania major)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L13aYA [auth H]222Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QFG2 (Leishmania major)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15ZA [auth M]204Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q6S3 (Leishmania major)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
eL13_chain_IAB [auth I]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AEA8 (Leishmania major)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18BB [auth P]198Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG98 (Leishmania major)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L19CB [auth Q]254Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QJ37 (Leishmania major)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aDB [auth R]179Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q5J4 (Leishmania major)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L9EB [auth E]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L17GB [auth T]166Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L21HB [auth S]159Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein L14IB [auth K]175Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11JB [auth D]188Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L27A/L29KB [auth L]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27LB [auth Y]134Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L28MB [auth Z]147Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L6NB [auth F]195Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L34OB [auth h]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein l35aPB [auth g]144Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23QB [auth J]139Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23aRB [auth V]145Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L26SB [auth W]143Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L22TB [auth U]129Leishmania major strain FriedlinMutation(s): 0 
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Find proteins for Q4Q0X2 (Leishmania major)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S Ribosomal protein L36UB [auth i]105Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L44VB [auth p]106Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aWB [auth o]92Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L24XB [auth X]124Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L38YB [auth k]83Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L39ZB [auth l]51Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41AC [auth n]34Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L1aBC [auth C]373Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal subunit protein L31DC [auth e]188Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37EC [auth j]83Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 15
MoleculeChains LengthOrganismImage
E-site_tRNA_chain_S4O [auth S4]19Leishmania major strain Friedlin
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Entity ID: 20
MoleculeChains LengthOrganismImage
SSU_rRNA_chain_S1T [auth S1]2,204Leishmania major strain Friedlin
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Entity ID: 41
MoleculeChains LengthOrganismImage
LSUa_rRNA_chain_1OA [auth 1]1,782Leishmania major strain Friedlin
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Entity ID: 42
MoleculeChains LengthOrganismImage
LSUb_rRNA_chain_2PA [auth 2]1,526Leishmania major strain Friedlin
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Entity ID: 43
MoleculeChains LengthOrganismImage
SR2_chain_4QA [auth 4]183Leishmania major strain Friedlin
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Entity ID: 44
MoleculeChains LengthOrganismImage
5.8S_rRNA_chain_7RA [auth 7]171Leishmania major strain Friedlin
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Entity ID: 46
MoleculeChains LengthOrganismImage
5S_rRNA_chain_8TA [auth 8]123Leishmania major strain Friedlin
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Entity ID: 47
MoleculeChains LengthOrganismImage
SR4_chain_5UA [auth 5]135Leishmania major strain Friedlin
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Entity ID: 58
MoleculeChains LengthOrganismImage
SR6_chain_6FB [auth 6]73Leishmania major strain Friedlin
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Entity ID: 81
MoleculeChains LengthOrganismImage
SR1_chain_3CC [auth 3]216Leishmania major strain Friedlin
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
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FD [auth Sb],
GC [auth Sc],
QH [auth o],
SH [auth j]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
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UF [auth 1],
VF [auth 1]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
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AD [auth S1]
AE [auth 1]
AF [auth 1]
AG [auth 2]
AH [auth 2]
AD [auth S1],
AE [auth 1],
AF [auth 1],
AG [auth 2],
AH [auth 2],
BD [auth S1],
BE [auth 1],
BF [auth 1],
BG [auth 2],
CD [auth S1],
CE [auth 1],
CF [auth 1],
CG [auth 2],
DD [auth S1],
DE [auth 1],
DF [auth 1],
DG [auth 2],
ED [auth SL],
EE [auth 1],
EF [auth 1],
EG [auth 2],
EH [auth 4],
FC [auth SS],
FE [auth 1],
FF [auth 1],
FG [auth 2],
FH [auth 4],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 2],
GH [auth 4],
HC [auth S1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 2],
HH [auth 7],
IC [auth S1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 2],
IH [auth 7],
JC [auth S1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 2],
JH [auth 7],
KC [auth S1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 2],
KH [auth 7],
LC [auth S1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 2],
LH [auth 8],
MC [auth S1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 2],
MH [auth 5],
NC [auth S1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 2],
NH [auth 6],
OC [auth S1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 2],
OH [auth T],
PC [auth S1],
PD [auth 1],
PE [auth 1],
PG [auth 2],
PH [auth J],
QC [auth S1],
QD [auth 1],
QE [auth 1],
QG [auth 2],
RC [auth S1],
RD [auth 1],
RE [auth 1],
RG [auth 2],
RH [auth 3],
SC [auth S1],
SD [auth 1],
SE [auth 1],
SG [auth 2],
TC [auth S1],
TD [auth 1],
TE [auth 1],
TG [auth 2],
UC [auth S1],
UD [auth 1],
UE [auth 1],
UG [auth 2],
VC [auth S1],
VD [auth 1],
VE [auth 1],
VG [auth 2],
WC [auth S1],
WD [auth 1],
WE [auth 1],
WF [auth 2],
WG [auth 2],
XC [auth S1],
XD [auth 1],
XE [auth 1],
XF [auth 2],
XG [auth 2],
YC [auth S1],
YD [auth 1],
YE [auth 1],
YF [auth 2],
YG [auth 2],
ZC [auth S1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 2],
ZG [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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BH [auth 2]
CH [auth 2]
DH [auth 2]
PF [auth 1]
QF [auth 1]
BH [auth 2],
CH [auth 2],
DH [auth 2],
PF [auth 1],
QF [auth 1],
RF [auth 1],
SF [auth 1],
TF [auth 1]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection