8A3W

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE

Rajan, K.S.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S9A [auth SD]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QIM3 (Leishmania major)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4B [auth SE]273Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG31 (Leishmania major)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth SF]265Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QDL5 (Leishmania major)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6D [auth SG]249Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q9NE83 (Leishmania major)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5E [auth SH]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q868B1 (Leishmania major)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7F [auth SI]200Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AC32 (Leishmania major)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15AG [auth SJ]130Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QGW3 (Leishmania major)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth SK]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for P25204 (Leishmania major)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S16I [auth SL]149Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q9A5 (Leishmania major)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S20J [auth SM]116Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q8G4 (Leishmania major)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S10K [auth SN]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1X7 (Leishmania major)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14L [auth SO]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q8H1 (Leishmania major)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S23M [auth SP]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QC89 (Leishmania major)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S18N [auth SR]153Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1Y2 (Leishmania major)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S29O [auth SS]57Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q817 (Leishmania major)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S13P [auth ST]151Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q3M1 (Leishmania major)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S11Q [auth SU]173Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S17R [auth SV]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q806 (Leishmania major)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15S [auth SW]152Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QBV0 (Leishmania major)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinT [auth SX]161Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AEE8 (Leishmania major)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S21U [auth SY]164Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QH01 (Leishmania major)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24V [auth SZ]137Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q1D2 (Leishmania major)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25W [auth Sa]120Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q9X4 (Leishmania major)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26X [auth Sb]112Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q8L6 (Leishmania major)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S27-1Y [auth Sc]86Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q140 (Leishmania major)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S33Z [auth Sd]87Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q931 (Leishmania major)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30AA [auth Se]66Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1BA [auth Sg]312Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aDA [auth SA]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4FX73 (Leishmania major)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAEA [auth SB]246Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q0Q0 (Leishmania major)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S3FA [auth SC]219Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q4A0 (Leishmania major)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Putative RNA binding proteinGA [auth Sh]235Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q5K7 (Leishmania major)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L3QA [auth B]419Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q2Q6 (Leishmania major)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L1aRA [auth C]373Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9ADW5 (Leishmania major)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L2SA [auth A]260Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4FWX5 (Leishmania major)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
uL30_chain_cTA [auth c]252Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q9H4 (Leishmania major)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L5UA [auth O]305Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for E9AF09 (Leishmania major)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15VA [auth M]204Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q6S3 (Leishmania major)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L13aWA [auth H]222Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QFG2 (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
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18YA [auth P]198Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QG98 (Leishmania major)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aZA [auth R]179Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q5J4 (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
Putative 60S ribosomal protein L19BB [auth Q]254Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QJ37 (Leishmania major)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L17CB [auth T]166Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QAX6 (Leishmania major)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L21DB [auth S]159Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QEX4 (Leishmania major)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L27A/L29EB [auth L]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L6FB [auth F]195Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q4D3 (Leishmania major)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L9GB [auth E]190Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27HB [auth Y]134Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32IB [auth f]133Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein l35aJB [auth g]144Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L35KB [auth a]127Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23LB [auth J]139Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L26MB [auth W]143Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23aNB [auth V]145Leishmania 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 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L28PB [auth Z]147Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein L14QB [auth K]175Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RB [auth j]83Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S Ribosomal protein L36SB [auth i]105Leishmania 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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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L44UB [auth p]106Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aVB [auth o]92Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11WB [auth D]188Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30XB [auth d]104Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L24YB [auth X]124Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29ZB [auth b]70Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L38AC [auth k]83Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L39BC [auth l]51Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41CC [auth n]34Leishmania major strain FriedlinMutation(s): 0 
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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: 29
MoleculeChains LengthOrganismImage
SSU_rRNA_chain_S1CA [auth S1]2,204Leishmania major strain Friedlin
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Entity ID: 34
MoleculeChains LengthOrganismImage
E-site_tRNA_chain_S4HA [auth S4]20Leishmania major strain Friedlin
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Entity ID: 35
MoleculeChains LengthOrganismImage
5S_rRNA_chain_8IA [auth 8]123Leishmania major strain Friedlin
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Entity ID: 36
MoleculeChains LengthOrganismImage
SR6_chain_6JA [auth 6]73Leishmania major strain Friedlin
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Entity ID: 37
MoleculeChains LengthOrganismImage
LSUb_rRNA_chain_2KA [auth 2]1,522Leishmania major strain Friedlin
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Entity ID: 38
MoleculeChains LengthOrganismImage
5.8S_rRNA_chain_7LA [auth 7]171Leishmania major strain Friedlin
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Entity ID: 39
MoleculeChains LengthOrganismImage
SR4_chain_5MA [auth 5]135Leishmania major strain Friedlin
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Entity ID: 40
MoleculeChains LengthOrganismImage
SR2_chain_4NA [auth 4]183Leishmania major strain Friedlin
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Entity ID: 41
MoleculeChains LengthOrganismImage
SR1_chain_3OA [auth 3]216Leishmania major strain Friedlin
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Entity ID: 42
MoleculeChains LengthOrganismImage
LSUa_rRNA_chain_1PA [auth 1]1,782Leishmania major strain Friedlin
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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GC [auth SS],
IC [auth Sb],
IJ [auth j],
JJ [auth o]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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BH [auth 1]
CH [auth 1]
DG [auth 4]
DH [auth 1]
HC [auth Sb]
BH [auth 1],
CH [auth 1],
DG [auth 4],
DH [auth 1],
HC [auth Sb],
OE [auth 8],
SE [auth 2],
TE [auth 2],
UE [auth 2],
VC [auth S1],
WC [auth S1],
XC [auth S1],
YC [auth S1]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth S1]
AF [auth 2]
AG [auth 7]
AH [auth 1]
AI [auth 1]
AD [auth S1],
AF [auth 2],
AG [auth 7],
AH [auth 1],
AI [auth 1],
BD [auth S1],
BF [auth 2],
BG [auth 7],
BI [auth 1],
CD [auth S1],
CF [auth 2],
CG [auth 5],
CI [auth 1],
DD [auth S1],
DF [auth 2],
DI [auth 1],
EC [auth SD],
ED [auth S1],
EF [auth 2],
EH [auth 1],
EI [auth 1],
FD [auth S1],
FF [auth 2],
FG [auth 3],
FH [auth 1],
FI [auth 1],
FJ [auth C],
GD [auth S1],
GF [auth 2],
GG [auth 1],
GH [auth 1],
GI [auth 1],
GJ [auth T],
HD [auth S1],
HF [auth 2],
HG [auth 1],
HH [auth 1],
HI [auth 1],
ID [auth S1],
IF [auth 2],
IG [auth 1],
IH [auth 1],
II [auth 1],
JC [auth S1],
JD [auth S1],
JF [auth 2],
JG [auth 1],
JH [auth 1],
KC [auth S1],
KD [auth S1],
KF [auth 2],
KG [auth 1],
KH [auth 1],
LC [auth S1],
LD [auth S1],
LF [auth 2],
LG [auth 1],
LH [auth 1],
MC [auth S1],
MD [auth S1],
MF [auth 2],
MG [auth 1],
MH [auth 1],
NC [auth S1],
ND [auth S1],
NF [auth 2],
NG [auth 1],
NH [auth 1],
OC [auth S1],
OD [auth S1],
OF [auth 2],
OG [auth 1],
OH [auth 1],
PC [auth S1],
PD [auth S1],
PE [auth 2],
PF [auth 2],
PG [auth 1],
PH [auth 1],
QC [auth S1],
QD [auth S1],
QE [auth 2],
QF [auth 2],
QG [auth 1],
QH [auth 1],
RC [auth S1],
RE [auth 2],
RG [auth 1],
RH [auth 1],
SC [auth S1],
SG [auth 1],
SH [auth 1],
TC [auth S1],
TG [auth 1],
TH [auth 1],
UC [auth S1],
UG [auth 1],
UH [auth 1],
VE [auth 2],
VG [auth 1],
VH [auth 1],
WE [auth 2],
WG [auth 1],
WH [auth 1],
XE [auth 2],
XG [auth 1],
XH [auth 1],
YE [auth 2],
YG [auth 1],
YH [auth 1],
ZC [auth S1],
ZE [auth 2],
ZG [auth 1],
ZH [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AE [auth S1]
AJ [auth 1]
BE [auth S1]
BJ [auth 1]
CE [auth S1]
AE [auth S1],
AJ [auth 1],
BE [auth S1],
BJ [auth 1],
CE [auth S1],
CJ [auth 1],
DE [auth S1],
DJ [auth 1],
EE [auth S1],
EG [auth 4],
EJ [auth 1],
FC [auth SO],
FE [auth S1],
GE [auth S1],
HE [auth S1],
HJ [auth J],
IE [auth S1],
JE [auth S1],
JI [auth 1],
KE [auth S1],
KI [auth 1],
LE [auth S1],
LI [auth 1],
ME [auth S1],
MI [auth 1],
NE [auth S1],
NI [auth 1],
OI [auth 1],
PI [auth 1],
QI [auth 1],
RD [auth S1],
RF [auth 2],
RI [auth 1],
SD [auth S1],
SF [auth 2],
SI [auth 1],
TD [auth S1],
TF [auth 2],
TI [auth 1],
UD [auth S1],
UF [auth 2],
UI [auth 1],
VD [auth S1],
VF [auth 2],
VI [auth 1],
WD [auth S1],
WF [auth 2],
WI [auth 1],
XD [auth S1],
XF [auth 2],
XI [auth 1],
YD [auth S1],
YF [auth 2],
YI [auth 1],
ZD [auth S1],
ZF [auth 2],
ZI [auth 1]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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: 2023-12-20
    Type: Initial release