SMTL ID : 3asj.1

Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

1 x XYN: 3-[(carboxymethyl)sulfanyl]-2-oxopropanoic acid(Non-covalent)

XYN.1: 11 residues within 4Å: Chain A: R.85, R.88, R.98, R.118, Y.125, D.228, D.232, V.259 Chain B: K.171, V.174, D.204 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.88, A:R.88, A:R.118, A:Y.125 Water bridges: A:N.96, A:R.98 Salt bridges: A:R.85, A:R.98, A:R.118, B:K.171

19 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: P.99, K.101, A.282, M.283, D.286, A.294, E.298 Ligand excluded by PLIP MPD.3: 9 residues within 4Å: Chain A: G.123, L.124, I.142, L.175, Q.179, T.223, N.224, L.225, L.226 Ligand excluded by PLIP MPD.4: 5 residues within 4Å: Chain A: T.121, E.122, S.143, K.145 Chain D: L.133 Ligand excluded by PLIP MPD.5: 6 residues within 4Å: Chain A: I.13, G.242, H.260, I.266, N.273, D.313 Ligand excluded by PLIP MPD.6: 3 residues within 4Å: Chain A: R.4, K.58, S.61 Ligand excluded by PLIP MPD.8: 10 residues within 4Å: Chain B: G.123, L.124, A.140, I.142, L.175, Q.179, T.223, N.224, L.225, L.226 Ligand excluded by PLIP MPD.9: 5 residues within 4Å: Chain B: K.101, M.283, A.294, E.298 Ligands: MPD.12 Ligand excluded by PLIP MPD.10: 6 residues within 4Å: Chain B: I.13, H.260, I.266, A.272, N.273, D.313 Ligand excluded by PLIP MPD.11: 7 residues within 4Å: Chain B: T.121, E.122, S.143, K.145, A.146 Chain C: Y.132, L.133 Ligand excluded by PLIP MPD.12: 4 residues within 4Å: Chain B: I.157, M.283, D.286 Ligands: MPD.9 Ligand excluded by PLIP MPD.13: 2 residues within 4Å: Chain B: E.54 Ligands: MPD.14 Ligand excluded by PLIP MPD.14: 5 residues within 4Å: Chain B: R.4, V.35, K.58, S.61 Ligands: MPD.13 Ligand excluded by PLIP MPD.15: 6 residues within 4Å: Chain C: R.85, R.88, R.118, Y.125, D.228 Chain D: K.171 Ligand excluded by PLIP MPD.16: 9 residues within 4Å: Chain C: G.123, L.124, A.140, T.178, Q.179, T.223, N.224, L.225, L.226 Ligand excluded by PLIP MPD.17: 7 residues within 4Å: Chain C: P.99, K.101, R.103, M.283, D.286, A.294, E.298 Ligand excluded by PLIP MPD.18: 7 residues within 4Å: Chain C: I.13, G.242, H.260, I.266, A.272, N.273, D.313 Ligand excluded by PLIP MPD.20: 9 residues within 4Å: Chain D: G.123, L.124, A.140, T.178, Q.179, T.223, N.224, L.225, L.226 Ligand excluded by PLIP MPD.21: 5 residues within 4Å: Chain D: G.242, H.260, A.272, N.273, D.313 Ligand excluded by PLIP MPD.22: 8 residues within 4Å: Chain D: P.99, L.279, A.282, M.283, D.286, A.294, K.295, E.298 Ligand excluded by PLIP

2 x XYM: (2Z)-3-[(carboxymethyl)sulfanyl]-2-hydroxyprop-2-enoic acid(Non-covalent)

XYM.7: 11 residues within 4Å: Chain A: K.171, V.174, D.204 Chain B: R.85, R.88, R.98, R.118, Y.125, D.228, D.232, V.259 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.88, B:R.88, B:R.118, B:D.228, A:D.204 Water bridges: B:N.96, B:R.98 Salt bridges: B:R.85, B:R.98, B:R.118, A:K.171 XYM.19: 9 residues within 4Å: Chain C: K.171, D.204 Chain D: R.88, R.98, R.118, Y.125, D.228, D.232, V.259 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.88, D:R.88, D:R.118, D:Y.125, D:D.228, C:D.204 Salt bridges: D:R.98, D:R.118, C:K.171 Water bridges: C:N.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nango, E. et al., Structure of Thermus thermophilus homoisocitrate dehydrogenase in complex with a designed inhibitor. J.Biochem. (2011)

Release Date

2011-09-21

Peptides

Homoisocitrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Homoisocitrate dehydrogenase

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