SMTL ID : 4zda.1

Crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.352, D.551, D.555 Ligands: ICT.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.352, A:D.551, A:D.555 MN.3: 4 residues within 4Å: Chain B: D.352, D.551, D.555 Ligands: ICT.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.352, B:D.551, B:D.555 MN.5: 4 residues within 4Å: Chain C: D.352, D.551, D.555 Ligands: ICT.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.352, C:D.551, C:D.555 MN.7: 4 residues within 4Å: Chain D: D.352, D.551, D.555 Ligands: ICT.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.352, D:D.551, D:D.555 MN.9: 4 residues within 4Å: Chain E: D.352, D.551, D.555 Ligands: ICT.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.352, E:D.551, E:D.555 MN.11: 4 residues within 4Å: Chain F: D.352, D.551, D.555 Ligands: ICT.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.352, F:D.551, F:D.555

6 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 13 residues within 4Å: Chain A: S.134, N.137, R.141, R.147, K.257, M.260, D.352, Y.422, R.550, D.551, D.555, A.585 Ligands: MN.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.134, A:N.137, A:R.141, A:K.257, A:Y.422, A:R.550 Salt bridges: A:R.141, A:R.141, A:R.147, A:K.257, A:K.257, A:R.550 ICT.4: 12 residues within 4Å: Chain B: S.134, N.137, R.141, R.147, K.257, M.260, D.352, Y.422, R.550, D.551, A.585 Ligands: MN.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.134, B:N.137, B:R.141, B:K.257, B:D.352, B:A.585 Salt bridges: B:R.141, B:R.141, B:R.147, B:K.257, B:K.257, B:R.550, B:R.550 ICT.6: 12 residues within 4Å: Chain C: S.134, N.137, R.141, R.147, K.257, M.260, D.352, Y.422, R.550, D.551, A.585 Ligands: MN.5 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.134, C:N.137, C:R.141, C:K.257, C:Y.422, C:A.585 Salt bridges: C:R.141, C:R.141, C:R.147, C:K.257, C:K.257, C:R.550, C:R.550 ICT.8: 12 residues within 4Å: Chain D: S.134, N.137, R.141, R.147, K.257, M.260, D.352, Y.422, R.550, D.551, A.585 Ligands: MN.7 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.134, D:N.137, D:K.257 Salt bridges: D:R.141, D:R.141, D:R.147, D:K.257, D:K.257, D:R.550, D:R.550 ICT.10: 12 residues within 4Å: Chain E: S.134, N.137, R.141, R.147, K.257, M.260, D.352, Y.422, R.550, D.551, A.585 Ligands: MN.9 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.134, E:N.137, E:R.141, E:K.257, E:A.585 Salt bridges: E:R.141, E:R.141, E:R.147, E:K.257, E:K.257, E:R.550 ICT.12: 12 residues within 4Å: Chain F: S.134, N.137, R.141, R.147, K.257, M.260, D.352, Y.422, R.550, D.551, A.585 Ligands: MN.11 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.134, F:N.137, F:K.257, F:Y.422, F:R.550 Salt bridges: F:R.141, F:R.141, F:R.147, F:K.257, F:K.257, F:R.550

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pojer, F. et al., crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis. To Be Published

Release Date

2016-06-29

Peptides

Isocitrate dehydrogenase (NADP) Icd2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Isocitrate dehydrogenase (NADP) Icd2