- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-hexamer
- Ligands
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.2: 16 residues within 4Å:- Chain A: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313
- Chain B: K.100, D.101, K.102, S.103, R.104
- Chain C: R.49, A.80
16 PLIP interactions:4 interactions with chain B, 10 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: B:R.104, A:Q.135, A:D.143, A:D.143, A:N.144, A:N.144, A:S.308, A:V.309, A:S.310
- Salt bridges: B:K.100, B:K.100, B:R.104, C:R.49, C:R.49
- pi-Stacking: A:F.313, A:F.313
ADP.5: 13 residues within 4Å:- Chain A: F.35, N.37, E.39
- Chain E: K.176
- Chain F: R.96, Q.97, K.99, D.101, K.102, H.130, D.224
- Ligands: MG.29, MG.30
12 PLIP interactions:3 interactions with chain A, 8 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: A:N.37, F:D.101
- pi-Stacking: A:F.35, A:F.35
- Water bridges: F:K.99, F:K.99, F:K.99, F:H.130
- Salt bridges: F:K.99, F:K.99, F:H.130, E:K.176
ADP.7: 16 residues within 4Å:- Chain A: K.100, D.101, K.102, S.103, R.104
- Chain B: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313
- Chain F: R.49, A.80
16 PLIP interactions:9 interactions with chain B, 3 interactions with chain F, 4 interactions with chain A- Hydrogen bonds: B:Q.135, B:D.143, B:N.144, B:N.144, B:S.308, B:V.309, B:S.310, F:A.80, A:R.104
- pi-Stacking: B:F.313, B:F.313
- Salt bridges: F:R.49, F:R.49, A:K.100, A:K.100, A:R.104
ADP.10: 13 residues within 4Å:- Chain B: F.35, N.37, E.39
- Chain C: R.96, Q.97, K.99, D.101, K.102, H.130, D.224
- Chain D: K.176
- Ligands: MG.14, MG.15
13 PLIP interactions:3 interactions with chain B, 9 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: B:N.37, C:D.101, C:D.101, C:D.224
- pi-Stacking: B:F.35, B:F.35
- Water bridges: C:K.99, C:K.99, C:K.99
- Salt bridges: C:K.99, C:K.99, C:H.130, D:K.176
ADP.11: 13 residues within 4Å:- Chain A: K.176
- Chain B: R.96, Q.97, K.99, D.101, K.102, H.130, D.224
- Chain C: F.35, N.37, E.39
- Ligands: MG.8, MG.9
12 PLIP interactions:8 interactions with chain B, 3 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: B:D.101, C:N.37
- Water bridges: B:K.99, B:K.99, B:K.99, B:H.130
- Salt bridges: B:K.99, B:K.99, B:H.130, A:K.176
- pi-Stacking: C:F.35, C:F.35
ADP.13: 16 residues within 4Å:- Chain C: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313
- Chain D: K.100, D.101, K.102, S.103, R.104
- Chain E: R.49, A.80
16 PLIP interactions:10 interactions with chain C, 2 interactions with chain E, 4 interactions with chain D- Hydrogen bonds: C:Q.135, C:D.143, C:D.143, C:N.144, C:N.144, C:S.308, C:V.309, C:S.310, D:R.104
- pi-Stacking: C:F.313, C:F.313
- Salt bridges: E:R.49, E:R.49, D:K.100, D:K.100, D:R.104
ADP.17: 16 residues within 4Å:- Chain B: R.49, A.80
- Chain C: K.100, D.101, K.102, S.103, R.104
- Chain D: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313
16 PLIP interactions:4 interactions with chain C, 9 interactions with chain D, 3 interactions with chain B- Hydrogen bonds: C:R.104, D:Q.135, D:D.143, D:N.144, D:N.144, D:S.308, D:V.309, D:S.310, B:A.80
- Salt bridges: C:K.100, C:K.100, C:R.104, B:R.49, B:R.49
- pi-Stacking: D:F.313, D:F.313
ADP.20: 13 residues within 4Å:- Chain D: F.35, N.37, E.39
- Chain E: R.96, Q.97, K.99, D.101, K.102, H.130, D.224
- Chain F: K.176
- Ligands: MG.24, MG.25
13 PLIP interactions:9 interactions with chain E, 1 interactions with chain F, 3 interactions with chain D- Hydrogen bonds: E:D.101, E:D.101, E:D.224, D:N.37
- Water bridges: E:K.99, E:K.99, E:K.99
- Salt bridges: E:K.99, E:K.99, E:H.130, F:K.176
- pi-Stacking: D:F.35, D:F.35
ADP.21: 13 residues within 4Å:- Chain C: K.176
- Chain D: R.96, Q.97, K.99, D.101, K.102, H.130, D.224
- Chain E: F.35, N.37, E.39
- Ligands: MG.18, MG.19
12 PLIP interactions:8 interactions with chain D, 3 interactions with chain E, 1 interactions with chain C- Hydrogen bonds: D:D.101, E:N.37
- Water bridges: D:K.99, D:K.99, D:K.99, D:H.130
- Salt bridges: D:K.99, D:K.99, D:H.130, C:K.176
- pi-Stacking: E:F.35, E:F.35
ADP.23: 16 residues within 4Å:- Chain A: R.49, A.80
- Chain E: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313
- Chain F: K.100, D.101, K.102, S.103, R.104
16 PLIP interactions:2 interactions with chain A, 10 interactions with chain E, 4 interactions with chain F- Salt bridges: A:R.49, A:R.49, F:K.100, F:K.100, F:R.104
- Hydrogen bonds: E:Q.135, E:D.143, E:D.143, E:N.144, E:N.144, E:S.308, E:V.309, E:S.310, F:R.104
- pi-Stacking: E:F.313, E:F.313
ADP.26: 13 residues within 4Å:- Chain A: R.96, Q.97, K.99, D.101, K.102, H.130, D.224
- Chain B: K.176
- Chain F: F.35, N.37, E.39
- Ligands: MG.3, MG.4
13 PLIP interactions:9 interactions with chain A, 3 interactions with chain F, 1 interactions with chain B- Hydrogen bonds: A:D.101, A:D.101, A:D.224, F:N.37
- Water bridges: A:K.99, A:K.99, A:K.99
- Salt bridges: A:K.99, A:K.99, A:H.130, B:K.176
- pi-Stacking: F:F.35, F:F.35
ADP.28: 16 residues within 4Å:- Chain D: R.49, A.80
- Chain E: K.100, D.101, K.102, S.103, R.104
- Chain F: Q.135, V.142, D.143, N.144, Y.146, S.308, V.309, S.310, F.313
16 PLIP interactions:3 interactions with chain D, 9 interactions with chain F, 4 interactions with chain E- Hydrogen bonds: D:A.80, F:Q.135, F:D.143, F:N.144, F:N.144, F:S.308, F:V.309, F:S.310, E:R.104
- Salt bridges: D:R.49, D:R.49, E:K.100, E:K.100, E:R.104
- pi-Stacking: F:F.313, F:F.313
- 12 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 3 residues within 4Å:- Chain A: K.99, H.130
- Ligands: ADP.26
4 PLIP interactions:1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:H.130, H2O.1, H2O.1, H2O.1
MG.4: 2 residues within 4Å:- Chain A: D.171
- Ligands: ADP.26
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:D.171
MG.8: 3 residues within 4Å:- Chain B: K.99, H.130
- Ligands: ADP.11
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:H.130, H2O.1, H2O.1, H2O.1
MG.9: 2 residues within 4Å:- Chain B: D.171
- Ligands: ADP.11
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:D.171
MG.14: 3 residues within 4Å:- Chain C: K.99, H.130
- Ligands: ADP.10
4 PLIP interactions:1 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:H.130, H2O.1, H2O.1, H2O.1
MG.15: 2 residues within 4Å:- Chain C: D.171
- Ligands: ADP.10
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:D.171
MG.18: 3 residues within 4Å:- Chain D: K.99, H.130
- Ligands: ADP.21
4 PLIP interactions:1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:H.130, H2O.1, H2O.1, H2O.1
MG.19: 2 residues within 4Å:- Chain D: D.171
- Ligands: ADP.21
1 PLIP interactions:1 interactions with chain D- Metal complexes: D:D.171
MG.24: 3 residues within 4Å:- Chain E: K.99, H.130
- Ligands: ADP.20
4 PLIP interactions:1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:H.130, H2O.1, H2O.1, H2O.1
MG.25: 2 residues within 4Å:- Chain E: D.171
- Ligands: ADP.20
1 PLIP interactions:1 interactions with chain E- Metal complexes: E:D.171
MG.29: 3 residues within 4Å:- Chain F: K.99, H.130
- Ligands: ADP.5
4 PLIP interactions:1 interactions with chain F, 3 Ligand-Water interactions- Metal complexes: F:H.130, H2O.1, H2O.1, H2O.1
MG.30: 2 residues within 4Å:- Chain F: D.171
- Ligands: ADP.5
1 PLIP interactions:1 interactions with chain F- Metal complexes: F:D.171
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hvorecny, K.L. et al., Human PRPS1 filaments stabilize allosteric sites to regulate activity. Nat.Struct.Mol.Biol. (2023)
- Release Date
- 2023-02-15
- Peptides
- Ribose-phosphate pyrophosphokinase 1: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-hexamer
- Ligands
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 12 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hvorecny, K.L. et al., Human PRPS1 filaments stabilize allosteric sites to regulate activity. Nat.Struct.Mol.Biol. (2023)
- Release Date
- 2023-02-15
- Peptides
- Ribose-phosphate pyrophosphokinase 1: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F