SMTL ID : 7cns.1

Crystal structure of Thermococcus kodakaraensis aconitase X (holo-form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PMV: (3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC ACID(Non-covalent)

PMV.1: 16 residues within 4Å: Chain A: A.47, G.48, V.49, S.50, N.53, N.79, P.80, E.129, S.130, V.345, K.361, Y.365 Chain B: S.63, T.64, V.65 Ligands: F3S.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.345 Hydrogen bonds: A:G.48, A:V.49, A:S.50, A:N.53, A:N.79, A:P.80, A:S.130, A:K.361, B:T.64, B:T.64 Water bridges: A:S.130 Salt bridges: A:K.361 PMV.3: 16 residues within 4Å: Chain C: A.47, G.48, V.49, S.50, N.53, N.79, P.80, E.129, S.130, V.345, K.361, Y.365 Chain D: S.63, T.64, V.65 Ligands: F3S.4 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:T.64, D:T.64, C:G.48, C:V.49, C:S.50, C:N.53, C:N.79, C:P.80, C:S.130, C:K.361 Hydrophobic interactions: C:V.345 Water bridges: C:S.130 Salt bridges: C:K.361

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 11 residues within 4Å: Chain A: P.80, C.110, E.129, S.131, G.282, C.283, P.284, C.342, V.344, K.361 Ligands: PMV.1 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.110, A:C.283, A:C.342 F3S.4: 11 residues within 4Å: Chain C: P.80, C.110, E.129, S.131, G.282, C.283, P.284, C.342, V.344, K.361 Ligands: PMV.3 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.110, C:C.283, C:C.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily. Commun Biol (2021)

Release Date

2021-06-16

Peptides

DUF521 domain-containing protein: AC
UPF0107 protein TK1248: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

DUF521 domain-containing protein

UPF0107 protein TK1248

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