- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x RUB: RIBULOSE-1,5-DIPHOSPHATE(Non-covalent)
- 2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.2: 5 residues within 4Å:- Chain A: E.227, Y.288
- Chain E: L.223, K.226, E.227
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:L.223, E:K.226
MPD.14: 5 residues within 4Å:- Chain B: L.223, K.226, E.227
- Chain D: E.227, Y.288
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.223, B:K.226
- Hydrogen bonds: B:Y.288
- 6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
AMP.3: 14 residues within 4Å:- Chain A: R.124, R.229, W.231, D.290
- Chain B: T.207, N.209, A.211, L.250, V.251, V.283, P.285, P.286
- Chain D: R.190, K.194
9 PLIP interactions:3 interactions with chain B, 2 interactions with chain D, 4 interactions with chain A- Hydrogen bonds: B:N.209, B:V.251, B:V.251, A:R.124, A:D.290
- Salt bridges: D:R.190, D:K.194, A:R.229
- Water bridges: A:R.124
AMP.6: 14 residues within 4Å:- Chain B: R.124, R.229, W.231, D.290
- Chain C: T.207, N.209, A.211, L.250, V.251, V.283, P.285, P.286
- Chain F: R.190, K.194
9 PLIP interactions:2 interactions with chain F, 4 interactions with chain B, 3 interactions with chain C- Salt bridges: F:R.190, F:K.194, B:R.229
- Hydrogen bonds: B:R.124, B:R.229, B:D.290, C:N.209, C:V.251, C:V.251
AMP.10: 14 residues within 4Å:- Chain A: T.207, N.209, A.211, L.250, V.251, V.283, P.285, P.286
- Chain C: R.124, R.229, W.231, D.290
- Chain E: R.190, K.194
12 PLIP interactions:5 interactions with chain C, 3 interactions with chain A, 4 interactions with chain E- Hydrogen bonds: C:R.124, C:R.229, C:D.290, A:N.209, A:V.251, A:V.251
- Water bridges: C:R.124, E:R.190, E:R.190
- Salt bridges: C:R.229, E:R.190, E:K.194
AMP.15: 14 residues within 4Å:- Chain A: R.190, K.194
- Chain D: R.124, R.229, W.231, D.290
- Chain E: T.207, N.209, A.211, L.250, V.251, V.283, P.285, P.286
10 PLIP interactions:4 interactions with chain D, 2 interactions with chain A, 4 interactions with chain E- Hydrogen bonds: D:R.124, D:D.290, E:N.209, E:V.251, E:V.251
- Water bridges: D:R.124, E:T.207
- Salt bridges: D:R.229, A:R.190, A:K.194
AMP.18: 14 residues within 4Å:- Chain C: R.190, K.194
- Chain E: R.124, R.229, W.231, D.290
- Chain F: T.207, N.209, A.211, L.250, V.251, V.283, P.285, P.286
9 PLIP interactions:2 interactions with chain C, 3 interactions with chain F, 4 interactions with chain E- Salt bridges: C:R.190, C:K.194, E:R.229
- Hydrogen bonds: F:N.209, F:V.251, F:V.251, E:R.124, E:R.229, E:D.290
AMP.22: 14 residues within 4Å:- Chain B: R.190, K.194
- Chain D: T.207, N.209, A.211, L.250, V.251, V.283, P.285, P.286
- Chain F: R.124, R.229, W.231, D.290
12 PLIP interactions:4 interactions with chain B, 5 interactions with chain F, 3 interactions with chain D- Water bridges: B:R.190, B:R.190, F:R.124
- Salt bridges: B:R.190, B:K.194, F:R.229
- Hydrogen bonds: F:R.124, F:R.229, F:D.290, D:N.209, D:V.251, D:V.251
- 6 x K: POTASSIUM ION(Non-covalent)
K.4: 4 residues within 4Å:- Chain A: M.193, K.194, T.196, V.230
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:K.194, A:T.196
K.7: 4 residues within 4Å:- Chain B: M.193, K.194, T.196, V.230
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:T.196
K.11: 4 residues within 4Å:- Chain C: M.193, K.194, T.196, V.230
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:T.196, H2O.10
K.16: 4 residues within 4Å:- Chain D: M.193, K.194, T.196, V.230
2 PLIP interactions:2 interactions with chain D- Metal complexes: D:K.194, D:T.196
K.19: 4 residues within 4Å:- Chain E: M.193, K.194, T.196, V.230
1 PLIP interactions:1 interactions with chain E- Metal complexes: E:T.196
K.23: 4 residues within 4Å:- Chain F: M.193, K.194, T.196, V.230
2 PLIP interactions:1 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:T.196, H2O.19
- 4 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)
G.8: 10 residues within 4Å:- Chain B: P.258, T.259, E.264, L.267, R.268, W.270, P.271, I.274, E.275, V.276
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain C- Hydrogen bonds: B:W.270, B:I.274, B:V.276, C:W.270, C:I.274, C:V.276
G.12: 8 residues within 4Å:- Chain C: E.264, L.267, R.268, W.270, P.271, I.274, E.275, V.276
Protein-ligand interaction information (PLIP) not availableG.20: 10 residues within 4Å:- Chain E: P.258, T.259, E.264, L.267, R.268, W.270, P.271, I.274, E.275, V.276
6 PLIP interactions:3 interactions with chain E, 3 interactions with chain F- Hydrogen bonds: E:W.270, E:I.274, E:V.276, F:W.270, F:I.274, F:V.276
G.24: 8 residues within 4Å:- Chain F: E.264, L.267, R.268, W.270, P.271, I.274, E.275, V.276
Protein-ligand interaction information (PLIP) not available- 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
AB
BC
CD
AE
BF
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x RUB: RIBULOSE-1,5-DIPHOSPHATE(Non-covalent)
- 2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
- 6 x K: POTASSIUM ION(Non-covalent)
- 4 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)
- 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
AB
BC
CD
AE
BF
C