SMTL ID : 5yfj.1

Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

RUB.1: 18 residues within 4Å: Chain A: M.19, R.22, G.23, A.24, G.25, R.65, C.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.23, A:A.24, A:G.25, A:S.137, A:K.138, A:A.139, A:Q.166, A:D.204, A:N.214, A:K.215 Water bridges: A:R.22, A:G.23, A:R.26, A:R.65, A:R.65, A:H.134, A:G.202, A:A.203, A:K.240, A:K.240 Salt bridges: A:R.22, A:R.65, A:K.215, A:K.240 RUB.6: 18 residues within 4Å: Chain B: M.19, R.22, G.23, A.24, G.25, R.65, C.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:G.23, B:A.24, B:G.25, B:K.138, B:A.139, B:Q.166, B:D.204, B:N.214, B:K.215 Water bridges: B:R.22, B:R.26, B:R.65, B:R.65, B:S.137, B:A.203, B:K.240, B:K.240 Salt bridges: B:R.22, B:R.65, B:K.215, B:K.240 RUB.10: 18 residues within 4Å: Chain C: M.19, R.22, G.23, A.24, G.25, R.65, C.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.23, C:A.24, C:G.25, C:K.138, C:A.139, C:Q.166, C:D.204, C:N.214, C:K.215 Water bridges: C:R.22, C:R.26, C:R.26, C:R.65, C:H.134, C:S.137, C:G.202, C:A.203, C:D.204, C:K.240, C:K.240 Salt bridges: C:R.22, C:R.65, C:K.215, C:K.240 RUB.13: 18 residues within 4Å: Chain D: M.19, R.22, G.23, A.24, G.25, R.65, C.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:G.23, D:A.24, D:G.25, D:S.137, D:K.138, D:A.139, D:Q.166, D:D.204, D:N.214, D:K.215 Water bridges: D:R.22, D:G.23, D:R.26, D:H.134, D:G.202, D:A.203, D:K.240, D:K.240 Salt bridges: D:R.22, D:R.65, D:K.215, D:K.240 RUB.18: 18 residues within 4Å: Chain E: M.19, R.22, G.23, A.24, G.25, R.65, C.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:G.23, E:A.24, E:G.25, E:K.138, E:A.139, E:Q.166, E:D.204, E:N.214, E:K.215 Water bridges: E:R.22, E:R.26, E:R.65, E:R.65, E:S.137, E:A.203, E:K.240, E:K.240 Salt bridges: E:R.22, E:R.65, E:K.215, E:K.240 RUB.22: 18 residues within 4Å: Chain F: M.19, R.22, G.23, A.24, G.25, R.65, C.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 24 PLIP interactions: 24 interactions with chain F Hydrogen bonds: F:G.23, F:A.24, F:G.25, F:K.138, F:A.139, F:Q.166, F:D.204, F:N.214, F:K.215 Water bridges: F:R.22, F:R.26, F:R.26, F:R.65, F:R.65, F:H.134, F:S.137, F:G.202, F:A.203, F:K.240, F:K.240 Salt bridges: F:R.22, F:R.65, F:K.215, F:K.240

6 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: M.193, K.194, T.196, V.230 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.193, A:K.194, A:T.196, H2O.4 K.7: 4 residues within 4Å: Chain B: M.193, K.194, T.196, V.230 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.193, B:K.194, B:T.196, H2O.13, H2O.13 K.11: 4 residues within 4Å: Chain C: M.193, K.194, T.196, V.230 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.193, C:K.194, C:T.196, H2O.18, H2O.18 K.14: 4 residues within 4Å: Chain D: M.193, K.194, T.196, V.230 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:M.193, D:K.194, D:T.196, H2O.23 K.19: 4 residues within 4Å: Chain E: M.193, K.194, T.196, V.230 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:M.193, E:K.194, E:T.196, H2O.32, H2O.32 K.23: 4 residues within 4Å: Chain F: M.193, K.194, T.196, V.230 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:M.193, F:K.194, F:T.196, H2O.37, H2O.38

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

CL.3: 1 residues within 4Å: Chain A: V.251 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: L.250, V.251 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: L.250, V.251 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain D: V.251 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain E: L.250, V.251 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain F: L.250, V.251 Ligand excluded by PLIP

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

PEG.4: 5 residues within 4Å: Chain A: P.258, L.267, I.274, E.275, V.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.276 PEG.9: 6 residues within 4Å: Chain B: Y.62, N.63, T.64, R.65, P.66, E.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.64 PEG.16: 5 residues within 4Å: Chain D: P.258, L.267, I.274, E.275, V.276 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.276 PEG.21: 6 residues within 4Å: Chain E: Y.62, N.63, T.64, R.65, P.66, E.252 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.64, E:E.252

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 3 residues within 4Å: Chain E: L.223, E.227, Y.288 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Water bridges: A:E.227 Hydrophobic interactions: E:L.223 MPD.17: 3 residues within 4Å: Chain B: L.223, E.227, Y.288 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.223 Hydrogen bonds: B:Y.288 Water bridges: D:E.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gogoi, P. et al., A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3. Sci Rep (2018)

Release Date

2018-02-14

Peptides

Ribose 1,5-bisphosphate isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Ribose 1,5-bisphosphate isomerase

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