SMTL ID : 6r6u.1

Crystal structure of human cis-aconitate decarboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

4 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.1: 12 residues within 4Å: Chain A: L.146, A.149, E.151, A.152, P.156, F.159, H.160, P.161, V.164, V.165, F.246, Y.247 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.151, A:A.152, A:V.164, A:Y.247, A:Y.247 Water bridges: A:E.151, A:K.157, A:K.157, A:F.159 BU3.5: 8 residues within 4Å: Chain A: A.241 Chain B: P.156, K.157, R.158, M.200, V.317, Q.318, Y.319 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.319, A:A.241 Hydrogen bonds: B:Q.318, B:Y.319 BU3.6: 3 residues within 4Å: Chain B: T.398, F.399, T.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.398 Water bridges: B:T.400 BU3.7: 13 residues within 4Å: Chain B: L.146, A.149, E.151, A.152, P.156, F.159, H.160, P.161, V.164, V.165, F.246, Y.247 Ligands: NA.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.151, B:A.152, B:V.164, B:Y.247 Hydrogen bonds: B:F.159 Water bridges: B:E.151, B:K.157

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: A.196, G.197, F.246 Chain B: A.196, G.197, F.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.196 NA.3: 3 residues within 4Å: Chain A: S.290, D.401, R.402 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.290, A:S.290, A:R.402 NA.4: 6 residues within 4Å: Chain A: E.240, G.244, A.245, Y.247, Y.250 Chain B: R.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.247, A:Y.247 NA.8: 6 residues within 4Å: Chain A: R.158 Chain B: E.240, G.244, A.245, Y.247, Y.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.247 NA.9: 5 residues within 4Å: Chain B: P.156, K.157, R.158, F.159 Ligands: BU3.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.157, B:R.158, B:F.159 Water bridges: B:E.151 NA.10: 3 residues within 4Å: Chain B: V.311, E.371, E.373 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.313, B:E.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, F. et al., Crystal structure ofcis-aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-09-25

Peptides

Cis-aconitate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cis-aconitate decarboxylase