Structure of PDB 5m3b Chain A Binding Site BS01

Receptor Information
>5m3b Chain A (length=228) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTLQGMNLE
RIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQL
APWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGK
ESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGKIPVIP
LTSDWFERASPRIILAAQQLCNALSQVD
Ligand information
Ligand IDCBY
InChIInChI=1S/C48H73N11O8.Co/c1-23(60)22-55-38(67)16-17-45(6)29(18-35(52)64)43-48(9)47(8,21-37(54)66)28(12-15-34(51)63)40(59-48)25(3)42-46(7,20-36(53)65)26(10-13-32(49)61)30(56-42)19-31-44(4,5)27(11-14-33(50)62)39(57-31)24(2)41(45)58-43;/h19,23,26-29,43,60H,10-18,20-22H2,1-9H3,(H14,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67);/q;+2/p-1/t23-,26-,27-,28-,29+,43-,45-,46+,47+,48+;/m1./s1
InChIKeyGFVWZOGCSKVPRA-JFYQDRLCSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1=C2[C@@]([C@@H](C3=[N]2[Co+2]45[N-]6[C@H]([C@@H]([C@@](C6=C(C7=[N]4C(=C3)C([C@@H]7CCC(=O)N)(C)C)C)(C)CCC(=O)NC[C@@H](C)O)CC(=O)N)[C@@]8([N]5=C1[C@H]([C@]8(C)CC(=O)N)CCC(=O)N)C)CCC(=O)N)(C)CC(=O)N
OpenEye OEToolkits 2.0.7CC1=C2C(C(C3[N-]2[Co+2]45[N]6=C1C(C(C6=CC7=[N]4C(=C(C8=[N]5C3(C(C8CCC(=O)N)(C)CC(=O)N)C)C)C(C7CCC(=O)N)(C)CC(=O)N)(C)C)CCC(=O)N)CC(=O)N)(C)CCC(=O)NCC(C)O
CACTVS 3.385[Co++].C[CH](O)CNC(=O)CC[C]1(C)[CH](CC(N)=O)[CH]2[N-]C1=C(C)C3=NC(=CC4=NC(=C(C)C5=N[C]2(C)[C](C)(CC(N)=O)[CH]5CCC(N)=O)[C](C)(CC(N)=O)[CH]4CCC(N)=O)C(C)(C)[CH]3CCC(N)=O
CACTVS 3.385[Co++].C[C@@H](O)CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)[C@H]2[N-]C1=C(C)C3=NC(=CC4=NC(=C(C)C5=N[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]5CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)C(C)(C)[C@@H]3CCC(N)=O
FormulaC48 H72 Co N11 O8
NameCOB(II)INAMIDE
ChEMBL
DrugBank
ZINC
PDB chain5m3b Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5m3b Conformational Change of a Tryptophan Residue in BtuF Facilitates Binding and Transport of Cobinamide by the Vitamin B12 Transporter BtuCD-F.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		P31 A32 Y50 W85 G87 F168 W196 S241 E245 R246
Binding residue
(residue number reindexed from 1)		P9 A10 Y28 W63 G65 F146 W174 S203 E207 R208
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=6.92,Kd=0.12uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0031419 cobalamin binding
Biological Process
GO:0015889 cobalamin transport
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m3b, PDBe:5m3b, PDBj:5m3b
PDBsum5m3b
PubMed28128319
UniProtP37028|BTUF_ECOLI Vitamin B12-binding protein (Gene Name=btuF)

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