SMTL ID : 2dj5.2 (1 other biounit)

Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.1, M.2 Chain C: G.1, M.2, R.3, D.36 Ligands: PO4.8, GOL.9 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.36, A:G.1 PO4.5: 3 residues within 4Å: Chain A: Y.112 Chain B: L.24, R.28 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.28 PO4.6: 4 residues within 4Å: Chain A: L.24, R.28 Chain B: Y.112 Chain D: G.126 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Salt bridges: A:R.28 Hydrogen bonds: B:Y.112, B:Y.112, D:G.126 PO4.7: 5 residues within 4Å: Chain A: Y.18 Chain B: F.69, I.70, S.71 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.70, B:S.71 Water bridges: B:S.71, B:G.73 PO4.8: 8 residues within 4Å: Chain A: G.1, M.2, R.3, D.36 Chain C: G.1, M.2 Ligands: PO4.1, GOL.2 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.1, A:D.36 PO4.12: 3 residues within 4Å: Chain C: Y.112 Chain D: L.24, R.28 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.28 Hydrogen bonds: C:Y.112 PO4.13: 4 residues within 4Å: Chain B: G.126 Chain C: L.24, R.28 Chain D: Y.112 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: B:G.126, D:Y.112, D:Y.112, D:Y.112 Salt bridges: C:R.28 PO4.14: 5 residues within 4Å: Chain C: Y.18 Chain D: F.69, I.70, S.71 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.70, D:S.71 Water bridges: D:S.71, D:G.73

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.3 Chain C: G.1 Ligands: PO4.8, GOL.9, GOL.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.1 GOL.3: 4 residues within 4Å: Chain A: F.69, I.70, S.71 Ligands: PO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.70, A:S.71 Water bridges: A:L.68 GOL.4: 2 residues within 4Å: Ligands: GOL.9, GOL.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.1 GOL.9: 5 residues within 4Å: Chain A: G.1 Chain C: R.3 Ligands: PO4.1, GOL.2, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.1 GOL.10: 4 residues within 4Å: Chain C: F.69, I.70, S.71 Ligands: PO4.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.70, C:S.71 Water bridges: C:L.68 GOL.11: 2 residues within 4Å: Ligands: GOL.2, GOL.4 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, J. et al., Crystal Structure of the Vitamin B(12) Biosynthetic Cobaltochelatase, CbiX (S), from Archaeoglobus Fulgidus. J.STRUCT.FUNCT.GENOM. (2006)

Release Date

2006-09-12

Peptides

Sirohydrochlorin cobaltochelatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Sirohydrochlorin cobaltochelatase

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