SMTL ID : 3a9c.1

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 in complex with ribulose-1,5-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x RUB: RIBULOSE-1,5-DIPHOSPHATE(Non-covalent)

RUB.1: 12 residues within 4Å: Chain A: C.149, H.150, S.151, K.152, A.153, Q.180, A.217, D.218, N.228, K.229, K.254, R.270 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.152, A:A.153, A:D.218, A:N.228, A:K.229 Water bridges: A:K.152, A:A.217, A:A.217 Salt bridges: A:K.152, A:K.229, A:K.254, A:R.270 RUB.4: 12 residues within 4Å: Chain B: C.149, S.151, K.152, A.153, K.178, Q.180, A.217, D.218, N.228, K.229, K.254, R.270 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.152, B:A.153, B:K.178, B:D.218, B:N.228, B:K.229 Water bridges: B:S.151, B:K.152, B:K.152, B:A.217 Salt bridges: B:K.152, B:K.229, B:K.254, B:R.270 RUB.7: 10 residues within 4Å: Chain C: C.149, S.151, K.152, A.153, Q.180, A.217, N.228, K.229, K.254, R.270 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.152, C:A.153, C:N.228, C:K.229 Water bridges: C:S.151, C:A.217 Salt bridges: C:K.152, C:K.229, C:K.254, C:R.270 RUB.9: 12 residues within 4Å: Chain D: C.149, H.150, S.151, K.152, A.153, Q.180, A.217, D.218, N.228, K.229, K.254, R.270 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.152, D:A.153, D:D.218, D:N.228, D:K.229 Water bridges: D:S.151, D:A.217, D:K.254, D:K.254 Salt bridges: D:K.152, D:K.229, D:K.254, D:R.270 RUB.11: 11 residues within 4Å: Chain E: C.149, H.150, S.151, K.152, A.153, Q.180, A.217, N.228, K.229, K.254, R.270 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:K.152, E:A.153, E:D.218, E:N.228, E:K.229 Water bridges: E:H.148, E:S.151, E:K.152, E:K.152, E:G.216, E:K.229, E:K.254 Salt bridges: E:K.152, E:K.229, E:K.254, E:R.270 RUB.13: 13 residues within 4Å: Chain F: C.149, H.150, S.151, K.152, A.153, K.178, Q.180, A.217, N.228, K.229, K.254, R.270, F.295 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:K.152, F:A.153, F:N.228, F:K.229 Water bridges: F:S.151, F:K.254 Salt bridges: F:K.152, F:K.178, F:K.229, F:K.254, F:R.270

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: K.240, R.243, V.244, E.301, D.304 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.301 Water bridges: A:K.240, A:R.243, A:R.243 PEG.5: 9 residues within 4Å: Chain B: A.239, K.240, R.243, V.244, W.245, T.246, E.301, Y.302, D.304 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.240, B:Y.302 PEG.8: 8 residues within 4Å: Chain C: K.240, R.243, V.244, W.245, T.246, E.301, Y.302, D.304 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.301 PEG.10: 7 residues within 4Å: Chain D: K.240, R.243, V.244, T.246, E.301, Y.302, D.304 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.240, D:R.243, D:Y.302 Water bridges: D:R.243 PEG.12: 5 residues within 4Å: Chain E: K.240, R.243, V.244, W.245, D.304 No protein-ligand interaction detected (PLIP) PEG.14: 7 residues within 4Å: Chain F: K.240, R.243, V.244, T.246, E.301, Y.302, D.304 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.240, F:R.243, F:Y.302 Water bridges: F:R.243

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.320 Chain E: D.320 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.320 MG.6: 3 residues within 4Å: Chain B: D.320 Chain D: D.320 Chain F: D.320 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, A. et al., Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1. J.Biol.Chem. (2012)

Release Date

2010-11-03

Peptides

Translation initiation factor eIF-2B, delta subunit: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Translation initiation factor eIF-2B, delta subunit

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