SMTL ID : 3vm6.1

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-hexamer

Ligands

6 x RI2: 1,5-di-O-phosphono-alpha-D-ribofuranose(Non-covalent)

RI2.1: 19 residues within 4Å: Chain A: M.33, R.36, G.37, A.38, G.39, I.41, R.79, S.149, H.150, S.151, K.152, A.153, Q.180, A.217, D.218, N.228, K.229, K.254, F.295 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.37, A:A.38, A:G.39, A:S.149, A:S.149, A:K.152, A:A.153, A:D.218, A:N.228, A:K.229 Water bridges: A:K.40, A:H.150, A:G.216, A:A.217, A:A.217, A:D.218, A:D.218 Salt bridges: A:R.36, A:R.36, A:R.79, A:K.229, A:K.229, A:K.254 RI2.7: 19 residues within 4Å: Chain B: M.33, R.36, G.37, A.38, G.39, R.79, S.149, H.150, S.151, K.152, A.153, Q.180, G.216, A.217, D.218, N.228, K.229, K.254, F.295 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.37, B:A.38, B:G.39, B:S.149, B:S.149, B:K.152, B:A.153, B:N.228, B:K.229 Water bridges: B:R.36, B:G.216, B:A.217, B:K.254 Salt bridges: B:R.36, B:R.36, B:R.79, B:K.229, B:K.229, B:K.254 RI2.13: 19 residues within 4Å: Chain C: M.33, R.36, G.37, A.38, G.39, I.41, R.79, S.149, H.150, S.151, K.152, A.153, Q.180, A.217, D.218, N.228, K.229, K.254, F.295 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.37, C:A.38, C:G.39, C:S.149, C:S.149, C:K.152, C:A.153, C:N.228, C:K.229 Water bridges: C:K.40, C:R.79, C:S.151, C:G.216, C:D.218 Salt bridges: C:R.36, C:R.79, C:K.229, C:K.229, C:K.254 RI2.20: 19 residues within 4Å: Chain D: M.33, R.36, G.37, A.38, G.39, I.41, R.79, S.149, H.150, S.151, K.152, A.153, Q.180, A.217, D.218, N.228, K.229, K.254, F.295 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:G.37, D:A.38, D:G.39, D:S.149, D:S.149, D:K.152, D:A.153, D:D.218, D:N.228, D:K.229 Water bridges: D:K.40, D:H.150, D:G.216, D:A.217, D:A.217 Salt bridges: D:R.36, D:R.36, D:R.79, D:K.229, D:K.229, D:K.254 RI2.26: 19 residues within 4Å: Chain E: M.33, R.36, G.37, A.38, G.39, R.79, S.149, H.150, S.151, K.152, A.153, Q.180, G.216, A.217, D.218, N.228, K.229, K.254, F.295 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:G.37, E:A.38, E:G.39, E:S.149, E:S.149, E:K.152, E:A.153, E:N.228, E:K.229 Water bridges: E:R.36, E:G.216, E:A.217, E:K.254 Salt bridges: E:R.36, E:R.36, E:R.79, E:K.229, E:K.229, E:K.254 RI2.32: 19 residues within 4Å: Chain F: M.33, R.36, G.37, A.38, G.39, I.41, R.79, S.149, H.150, S.151, K.152, A.153, Q.180, A.217, D.218, N.228, K.229, K.254, F.295 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.37, F:A.38, F:G.39, F:S.149, F:S.149, F:K.152, F:A.153, F:N.228, F:K.229 Water bridges: F:K.40, F:R.79, F:R.79, F:S.151, F:G.216 Salt bridges: F:R.36, F:R.79, F:K.229, F:K.229, F:K.254

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

PEG.2: 7 residues within 4Å: Chain A: A.239, K.240, R.243, V.244, W.245, T.246, D.304 Ligand excluded by PLIP PEG.3: 5 residues within 4Å: Chain A: G.142, V.144, D.167, K.169, M.209 Ligand excluded by PLIP PEG.4: 4 residues within 4Å: Chain A: W.162, G.165, K.166, D.167 Ligand excluded by PLIP PEG.8: 8 residues within 4Å: Chain A: P.299 Chain B: K.240, R.243, V.244, W.245, D.304 Chain D: R.204, K.208 Ligand excluded by PLIP PEG.10: 2 residues within 4Å: Chain B: W.162, G.165 Ligand excluded by PLIP PEG.11: 7 residues within 4Å: Chain B: K.208, T.210, H.242, V.244 Chain D: M.207, K.208, T.210 Ligand excluded by PLIP PEG.14: 7 residues within 4Å: Chain B: P.299 Chain C: K.240, R.243, V.244, W.245, D.304 Chain F: R.204 Ligand excluded by PLIP PEG.15: 3 residues within 4Å: Chain C: D.167, I.168, K.169 Ligand excluded by PLIP PEG.16: 5 residues within 4Å: Chain C: W.162, E.163, G.165, K.166, D.167 Ligand excluded by PLIP PEG.17: 4 residues within 4Å: Chain C: M.269, R.270, W.291, N.292 Ligand excluded by PLIP PEG.21: 7 residues within 4Å: Chain D: A.239, K.240, R.243, V.244, W.245, T.246, D.304 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain D: G.142, V.144, D.167, K.169, M.209 Ligand excluded by PLIP PEG.23: 4 residues within 4Å: Chain D: W.162, G.165, K.166, D.167 Ligand excluded by PLIP PEG.27: 8 residues within 4Å: Chain A: R.204, K.208 Chain D: P.299 Chain E: K.240, R.243, V.244, W.245, D.304 Ligand excluded by PLIP PEG.29: 2 residues within 4Å: Chain E: W.162, G.165 Ligand excluded by PLIP PEG.30: 7 residues within 4Å: Chain A: M.207, K.208, T.210 Chain E: K.208, T.210, H.242, V.244 Ligand excluded by PLIP PEG.33: 7 residues within 4Å: Chain C: R.204 Chain E: P.299 Chain F: K.240, R.243, V.244, W.245, D.304 Ligand excluded by PLIP PEG.34: 3 residues within 4Å: Chain F: D.167, I.168, K.169 Ligand excluded by PLIP PEG.35: 5 residues within 4Å: Chain F: W.162, E.163, G.165, K.166, D.167 Ligand excluded by PLIP PEG.36: 4 residues within 4Å: Chain F: M.269, R.270, W.291, N.292 Ligand excluded by PLIP

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: K.178, Q.180, K.229 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: E.34, I.35, R.36, K.40 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: K.178, K.229 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: K.178, Q.180, K.229 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain E: E.34, I.35, R.36, K.40 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain F: K.178, K.229 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: D.320 Chain B: D.320 Chain C: D.320 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.320, C:D.320, A:D.320, B:D.320 MG.19: 3 residues within 4Å: Chain C: K.208 Chain F: K.208 Ligands: MG.38 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Metal complexes: F:K.208, C:K.208 MG.25: 3 residues within 4Å: Chain D: D.320 Chain E: D.320 Chain F: D.320 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E, 1 interactions with chain D Metal complexes: F:D.320, F:D.320, E:D.320, D:D.320 MG.38: 3 residues within 4Å: Chain C: K.208 Chain F: K.208 Ligands: MG.19 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Metal complexes: F:K.208, C:K.208

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain B: V.144, K.169, P.194, M.209 Chain F: N.287, E.289, W.291 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:K.169, F:N.287 PG4.28: 7 residues within 4Å: Chain C: N.287, E.289, W.291 Chain E: V.144, K.169, P.194, M.209 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:K.169, C:N.287

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

2012-04-25

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Translation initiation factor eIF-2B, delta subunit