SMTL ID : 7lub.1

Crystal structure of recombinant human fumarase in complex with D-2-amino-3-phosphono-propionic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x APO: D-2-AMINO-3-PHOSPHONO-PROPIONIC ACID(Non-covalent)

APO.1: 13 residues within 4Å: Chain A: S.101, T.103, S.142, S.143, N.144 Chain B: T.190, H.191 Chain C: S.321, I.323, M.324, K.327, N.329 Ligands: GOL.2 11 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:S.321, C:N.329, A:S.101, A:T.103, A:S.143, A:N.144, A:N.144, B:T.190, B:H.191 Salt bridges: C:K.327, B:H.191 APO.5: 12 residues within 4Å: Chain B: S.321, I.323, M.324, K.327, N.329 Chain C: T.190, H.191 Chain D: S.101, T.103, S.142, S.143, N.144 13 PLIP interactions: 6 interactions with chain D, 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:S.101, D:T.103, D:S.143, D:N.144, B:N.329, C:T.190, C:H.191 Water bridges: D:N.106, D:N.106, B:S.322, B:I.323 Salt bridges: B:K.327, C:H.191 APO.6: 13 residues within 4Å: Chain A: S.321, I.323, M.324, K.327, N.329 Chain C: S.101, T.103, S.142, S.143, N.144 Chain D: T.190, H.191 Ligands: GOL.7 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: C:S.101, C:S.143, C:N.144, C:N.144, A:S.321, A:N.329, D:T.190, D:H.191 Salt bridges: A:K.327, D:H.191 APO.10: 12 residues within 4Å: Chain A: T.190, H.191 Chain B: S.101, T.103, S.142, S.143, N.144 Chain D: S.321, I.323, M.324, K.327, N.329 14 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A, 7 interactions with chain B Hydrogen bonds: D:N.329, A:T.190, A:H.191, B:S.101, B:T.103, B:T.103, B:S.143, B:N.144 Water bridges: D:S.322, D:I.323, B:N.106, B:N.106 Salt bridges: D:K.327, A:H.191

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: Q.27, N.106, M.107, N.134, N.138, S.142, S.143 Chain C: S.321, S.322, I.323 Ligands: APO.1 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:S.321, C:S.322, C:I.323, A:Q.27, A:N.106, A:N.134, A:N.134, A:N.138, A:S.143 GOL.3: 2 residues within 4Å: Chain A: T.263, P.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.263 Water bridges: A:E.227 GOL.4: 8 residues within 4Å: Chain A: R.217, A.221, E.279 Chain B: R.217, A.220, A.221, E.279, A.283 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.279, B:E.279, A:R.217, A:E.279, A:E.279 GOL.7: 11 residues within 4Å: Chain A: S.321, S.322, I.323 Chain C: Q.27, N.106, M.107, N.134, N.138, S.142, S.143 Ligands: APO.6 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.27, C:N.106, C:N.134, C:N.134, C:N.138, C:S.143, A:S.321, A:S.322, A:I.323 GOL.8: 2 residues within 4Å: Chain C: T.263, P.265 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.263 GOL.9: 8 residues within 4Å: Chain C: R.217, A.221, E.279 Chain D: R.217, A.220, A.221, E.279, A.283 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.217, C:E.279, D:E.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hicks, K.G. et al., Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science (2023)

Release Date

2022-02-23

Peptides

Fumarate hydratase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Fumarate hydratase, mitochondrial

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