SMTL ID : 8dpb.1

MeaB in complex with the cobalamin-binding domain of its target mutase with GMPPCP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 22 residues within 4Å: Chain A: P.64, G.65, V.66, G.67, K.68, S.69, T.70, D.105, R.108, E.154, G.157, N.201, K.202, D.204, S.241, G.242, L.243 Chain B: G.181, D.182, Q.185, K.188 Ligands: MG.2 22 PLIP interactions: 4 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:D.182, B:Q.185, A:G.65, A:V.66, A:G.67, A:K.68, A:K.68, A:K.68, A:S.69, A:T.70, A:T.70, A:G.157, A:N.201, A:K.202, A:K.202, A:G.242, A:L.243 Water bridges: B:K.188, B:K.188, A:T.70 Salt bridges: A:R.108, A:D.204 GCP.5: 21 residues within 4Å: Chain A: D.182, Q.185, K.188 Chain B: P.64, G.65, V.66, G.67, K.68, S.69, T.70, D.105, R.108, E.154, G.157, N.201, K.202, D.204, S.241, G.242, L.243 Ligands: MG.6 22 PLIP interactions: 3 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:D.182, A:Q.185, B:G.65, B:V.66, B:G.67, B:K.68, B:K.68, B:K.68, B:S.69, B:T.70, B:T.70, B:E.154, B:G.157, B:N.201, B:K.202, B:K.202, B:G.242, B:L.243 Water bridges: A:K.188, B:D.105 Salt bridges: B:R.108, B:D.204

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.69, D.105, E.154 Ligands: GCP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.69, A:D.105, A:E.154, H2O.1 MG.6: 5 residues within 4Å: Chain A: K.188 Chain B: S.69, D.105, E.154 Ligands: GCP.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.69, B:D.105, B:E.154, H2O.2

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: P.6, L.11, A.21, R.25 Chain C: R.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.140, C:R.140 GOL.4: 6 residues within 4Å: Chain A: G.18, R.20, K.85, A.146, G.147, F.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.18, A:R.20, A:K.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaccaro, F.A. et al., Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-03-01

Peptides

Methylmalonyl-CoA mutase accessory protein: AB
Methylmalonyl-CoA mutase, alpha subunit: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Methylmalonyl-CoA mutase accessory protein

Methylmalonyl-CoA mutase, alpha subunit