Structure of PDB 4fdv Chain A Binding Site BS01

Receptor Information

>4fdv Chain A (length=208) Species: 272942 (Rhodobacter capsulatus SB 1003)

PHEYEKDGAKIYVQSFATIRAEADLARFTPEEEVVVVRMIHAAGMVGLEN
HVRFAPGMAIAARAALEAGAPILCDARMVSEGITRARLPAKNEVICTLQD
PRVPALAQEMGNTRSAAALELWRPKLEGAVVAIGNAPTALFHLLNMLEDP
ACPRPAAIIGCPVGFIGAAESKAALAVANPVPWVIVEGRLGGSAITVAAV
NALACRKE

Ligand information

• Ligand ID: 0UK
• InChI: InChI=1S/C45H62N4O14/c1-21-36-24(10-13-30(52)53)41(3,4)28(47-36)18-27-23(9-12-29(50)51)43(6,19-34(60)61)39(46-27)22(2)37-25(11-14-31(54)55)44(7,20-35(62)63)45(8,49-37)40-26(17-33(58)59)42(5,38(21)48-40)16-15-32(56)57/h18,21,23-26,36,40,47H,9-17,19-20H2,1-8H3,(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/b28-18-,39-22-/t21-,23-,24+,25-,26+,36-,40-,42-,43+,44+,45+/m1/s1
• InChIKey: YHLYHOGUCOLFRO-ZWMNGWNLSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C[C@@H]1[C@@H]2[C@@H](C(/C(=C/C3=N/C(=C(\C4=N[C@@]([C@H]5[C@@H]([C@@](C1=N5)(C)CCC(=O)O)CC(=O)O)([C@@]([C@@H]4CCC(=O)O)(C)CC(=O)O)C)/C)/[C@@]([C@@H]3CCC(=O)O)(C)CC(=O)O)/N2)(C)C)CCC(=O)O
  OpenEye OEToolkits 1.7.6: CC1C2C(C(C(=CC3=NC(=C(C4=NC(C5C(C(C1=N5)(C)CCC(=O)O)CC(=O)O)(C(C4CCC(=O)O)(C)CC(=O)O)C)C)C(C3CCC(=O)O)(C)CC(=O)O)N2)(C)C)CCC(=O)O
  CACTVS 3.370: C[C@@H]1[C@H]2NC(=C\C3=NC(=C(C)/C4=N[C@@](C)([C@@H]5N=C1[C@](C)(CCC(O)=O)[C@H]5CC(O)=O)[C@@](C)(CC(O)=O)[C@@H]4CCC(O)=O)\[C@@](C)(CC(O)=O)[C@@H]3CCC(O)=O)/C(C)(C)[C@H]2CCC(O)=O
  CACTVS 3.370: C[CH]1[CH]2NC(=CC3=NC(=C(C)C4=N[C](C)([CH]5N=C1[C](C)(CCC(O)=O)[CH]5CC(O)=O)[C](C)(CC(O)=O)[CH]4CCC(O)=O)[C](C)(CC(O)=O)[CH]3CCC(O)=O)C(C)(C)[CH]2CCC(O)=O
• Formula: C45 H62 N4 O14
• ZINC: ZINC000263621269
• PDB chain: 4fdv Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4fdv An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
• Resolution: 1.68 Å
• Binding residue (original residue number in PDB): I12 Y13 S16 R39 H42 T85 A195 N202
• Binding residue (residue number reindexed from 1): I11 Y12 S15 R38 H41 T84 A194 N201
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): H42
• Catalytic site (residue number reindexed from 1): H41
• Enzyme Commision number: 5.4.1.2: Transferred entry: 5.4.99.61.

Gene Ontology

Molecular Function

• GO:0016853 isomerase activity
• GO:0016993 precorrin-8X methylmutase activity

Biological Process

• GO:0009236 cobalamin biosynthetic process

External links

• PDB: RCSB:4fdv, PDBe:4fdv, PDBj:4fdv
• PDBsum: 4fdv
• PubMed: 23042036
• UniProt: D5AV08