SMTL ID : 3a11.1

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

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

PEG.1: 6 residues within 4Å: Chain A: A.239, K.240, R.243, V.244, Y.302, D.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.302 Water bridges: A:R.243 PEG.2: 10 residues within 4Å: Chain B: A.239, K.240, R.243, V.244, W.245, T.246, E.301, Y.302, V.303, D.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.240, B:Y.302 Water bridges: B:W.245 PEG.4: 7 residues within 4Å: Chain C: K.240, R.243, V.244, W.245, E.301, Y.302, D.304 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.301 PEG.5: 7 residues within 4Å: Chain D: A.239, K.240, R.243, V.244, T.246, 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.6: 5 residues within 4Å: Chain A: P.299, E.301, Y.302 Chain E: K.240, R.243 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:E.301, E:K.240 PEG.8: 8 residues within 4Å: Chain D: L.261 Chain F: K.240, R.243, V.244, E.301, Y.302, V.303, D.304 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.240, F:E.301

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: D.320 Chain D: D.320, R.323 Chain F: D.320 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.320, H2O.6 MG.7: 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

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

2010-03-31

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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