SMTL ID : 1cw4.1

CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.307, D.311 Chain B: D.283 Ligands: AKG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.307, H2O.3, H2O.13 MN.4: 4 residues within 4Å: Chain A: D.283 Chain B: D.307, D.311 Ligands: AKG.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.307, H2O.16, H2O.26

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: V.107, G.108, G.109, G.110, I.111 Chain B: K.235 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.108, A:G.110, A:I.111 Water bridges: A:G.109 Salt bridges: B:K.235 SO4.5: 6 residues within 4Å: Chain A: K.235 Chain B: V.107, G.108, G.109, G.110, I.111 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.108, B:G.110, B:I.111 Water bridges: B:G.109 Salt bridges: A:K.235

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 10 residues within 4Å: Chain A: S.113, N.115, V.116, R.119, R.129, R.153, Y.160, D.307 Chain B: I.233 Ligands: MN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.115 Hydrogen bonds: A:S.113, A:N.115, A:Y.160, A:D.307 Water bridges: A:R.129, A:R.129, A:R.129, A:R.153, A:Y.160 Salt bridges: A:R.119, A:R.129, A:R.153 AKG.6: 10 residues within 4Å: Chain A: I.233 Chain B: S.113, N.115, V.116, R.119, R.129, R.153, Y.160, D.307 Ligands: MN.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.115 Hydrogen bonds: B:S.113, B:N.115, B:Y.160, B:Y.160 Water bridges: B:R.129, B:R.129, B:R.129, B:R.153 Salt bridges: B:R.119, B:R.129, B:R.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherbavaz, D.B. et al., Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. J.Mol.Biol. (2000)

Release Date

1999-09-01

Peptides

ISOCITRATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ISOCITRATE DEHYDROGENASE

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