SMTL ID : 5yfs.1

Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

RI2.1: 18 residues within 4Å: Chain A: M.19, R.22, G.23, A.24, G.25, R.65, S.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.23, A:A.24, A:G.25, A:S.135, A:S.137, A:K.138, A:A.139, A:Q.166, 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.22, A:R.65, A:K.215, A:K.215, A:K.240 RI2.5: 19 residues within 4Å: Chain B: M.19, R.22, G.23, A.24, G.25, I.27, R.65, S.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:G.23, B:A.24, B:G.25, B:S.135, B:K.138, B:A.139, B:Q.166, B:N.214, B:K.215 Water bridges: B:R.22, B:G.23, B:R.26, B:R.65, B:R.65, B:H.134, B:S.137, B:G.202, B:A.203, B:K.240, B:K.240 Salt bridges: B:R.22, B:R.22, B:R.65, B:K.215, B:K.215, B:K.240 RI2.8: 19 residues within 4Å: Chain C: M.19, R.22, G.23, A.24, G.25, I.27, R.65, S.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:G.23, C:A.24, C:G.25, C:S.135, C:S.135, C:K.138, C:A.139, C:Q.166, C:N.214, C:K.215 Water bridges: C:R.22, C:R.26, C:R.65, C:S.137, C:S.137, C:G.202, C:D.204 Salt bridges: C:R.22, C:R.22, C:R.65, C:K.215, C:K.215, C:K.240 RI2.11: 18 residues within 4Å: Chain D: M.19, R.22, G.23, A.24, G.25, R.65, S.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:G.23, D:A.24, D:G.25, D:S.135, D:S.137, D:K.138, D:A.139, D:Q.166, D:N.214, D:K.215 Water bridges: D:R.22, D:G.23, D:R.26, D:R.65, D:H.134, D:G.202, D:A.203, D:D.204, D:K.240, D:K.240 Salt bridges: D:R.22, D:R.22, D:R.65, D:K.215, D:K.215, D:K.240 RI2.15: 19 residues within 4Å: Chain E: M.19, R.22, G.23, A.24, G.25, I.27, R.65, S.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 26 PLIP interactions: 26 interactions with chain E Hydrogen bonds: E:G.23, E:A.24, E:G.25, E:S.135, E:K.138, E:A.139, E:Q.166, E:N.214, E:K.215 Water bridges: E:R.22, E:G.23, E:R.26, E:H.134, E:S.137, E:G.202, E:A.203, E:D.204, E:D.204, E:K.240, E:K.240 Salt bridges: E:R.22, E:R.22, E:R.65, E:K.215, E:K.215, E:K.240 RI2.18: 19 residues within 4Å: Chain F: M.19, R.22, G.23, A.24, G.25, I.27, R.65, S.135, H.136, S.137, K.138, A.139, Q.166, A.203, D.204, N.214, K.215, K.240, F.281 23 PLIP interactions: 23 interactions with chain F Hydrogen bonds: F:G.23, F:A.24, F:G.25, F:S.135, F:S.135, F:K.138, F:A.139, F:Q.166, F:N.214, F:K.215 Water bridges: F:R.22, F:R.26, F:R.65, F:R.65, F:S.137, F:S.137, F:G.202 Salt bridges: F:R.22, F:R.22, F:R.65, F:K.215, 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 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.194, A:T.196, H2O.6 K.6: 4 residues within 4Å: Chain B: M.193, K.194, T.196, V.230 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.193, B:K.194, B:T.196, H2O.14 K.9: 4 residues within 4Å: Chain C: M.193, K.194, T.196, V.230 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.193, C:K.194, C:T.196, H2O.20 K.12: 4 residues within 4Å: Chain D: M.193, K.194, T.196, V.230 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.194, D:T.196, H2O.30 K.16: 4 residues within 4Å: Chain E: M.193, K.194, T.196, V.230 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:M.193, E:K.194, E:T.196, H2O.37 K.19: 4 residues within 4Å: Chain F: M.193, K.194, T.196, V.230 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:M.193, F:K.194, F:T.196, H2O.44

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

CL.3: 2 residues within 4Å: Chain A: L.250, V.251 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: L.250, V.251 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: L.250, V.251 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain D: L.250, V.251 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain E: L.250, V.251 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain F: L.250, V.251 Ligand excluded by PLIP

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

MPD.4: 6 residues within 4Å: Chain A: L.223, E.227 Chain F: L.223, K.226, E.227, Y.288 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:L.223, F:K.226, A:L.223 MPD.14: 6 residues within 4Å: Chain C: L.223, K.226, E.227, Y.288 Chain D: L.223, E.227 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.223, C:L.223, C:K.226

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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