SMTL ID : 6d9s.1

The (p)ppGpp-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

4 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.1: 20 residues within 4Å: Chain A: L.45, K.46, G.47, D.103, I.104, I.105, D.106, S.107, G.108, L.109, T.110, K.134, E.154, F.155, V.156, V.157, L.161, D.162, R.168 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.46, A:G.47, A:D.103, A:D.106, A:S.107, A:S.107, A:G.108, A:L.109, A:T.110, A:K.134, A:V.156, A:V.156, A:V.156, A:D.162 Water bridges: A:R.168, A:R.168, A:R.168, A:R.168 Salt bridges: A:R.168 G4P.7: 20 residues within 4Å: Chain B: L.45, K.46, G.47, D.103, I.104, I.105, D.106, S.107, G.108, L.109, T.110, K.134, E.154, F.155, V.156, V.157, L.161, D.162, R.168 Ligands: MG.8 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:L.45, B:K.46, B:G.47, B:D.103, B:I.104, B:D.106, B:D.106, B:S.107, B:S.107, B:S.107, B:G.108, B:K.134, B:V.156, B:V.156, B:V.156, B:D.162 Water bridges: B:A.48, B:T.110, B:D.162, B:R.168, B:R.168, B:R.168, B:R.168 Salt bridges: B:R.168 G4P.11: 20 residues within 4Å: Chain C: L.45, K.46, G.47, D.103, I.104, I.105, D.106, S.107, G.108, L.109, T.110, K.134, E.154, F.155, V.156, V.157, L.161, D.162, R.168 Ligands: MG.12 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:K.46, C:G.47, C:D.103, C:D.106, C:D.106, C:S.107, C:S.107, C:G.108, C:L.109, C:T.110, C:K.134, C:V.156, C:V.156, C:V.156, C:D.162 Water bridges: C:R.168, C:R.168, C:R.168, C:R.168 Salt bridges: C:R.168 G4P.17: 20 residues within 4Å: Chain D: L.45, K.46, G.47, D.103, I.104, I.105, D.106, S.107, G.108, L.109, T.110, K.134, E.154, F.155, V.156, V.157, L.161, D.162, R.168 Ligands: MG.18 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:L.45, D:K.46, D:G.47, D:D.103, D:I.104, D:D.106, D:S.107, D:S.107, D:S.107, D:G.108, D:K.134, D:V.156, D:V.156, D:V.156, D:D.162 Water bridges: D:A.48, D:T.110, D:D.162, D:R.168, D:R.168, D:R.168, D:R.168 Salt bridges: D:R.168

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.162, R.168 Ligands: G4P.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.162, H2O.1, H2O.2, H2O.2 MG.8: 3 residues within 4Å: Chain B: D.162, R.168 Ligands: G4P.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.162, B:D.162, H2O.3, H2O.3, H2O.4 MG.12: 3 residues within 4Å: Chain C: D.162, R.168 Ligands: G4P.11 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.162, H2O.6, H2O.6, H2O.7 MG.18: 3 residues within 4Å: Chain D: D.162, R.168 Ligands: G4P.17 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.162, D:D.162, H2O.7, H2O.8, H2O.9

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

PEG.3: 6 residues within 4Å: Chain A: N.6, I.9, E.10, K.11, V.12, Y.172 No protein-ligand interaction detected (PLIP) PEG.4: 9 residues within 4Å: Chain A: D.33, Y.34, N.36, T.37, D.97, K.124, S.125, K.127, Y.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.124 PEG.5: 7 residues within 4Å: Chain A: D.8, Y.163, K.164, Q.166, Y.167, V.180 Chain D: Y.62 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.62 PEG.6: 5 residues within 4Å: Chain A: V.38, E.64, G.95, R.96 Chain D: Q.166 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.95 PEG.9: 6 residues within 4Å: Chain B: N.6, I.9, E.10, K.11, V.12, Y.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.10 PEG.10: 8 residues within 4Å: Chain B: D.33, Y.34, T.37, D.97, K.124, S.125, K.127, Y.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.33 PEG.13: 6 residues within 4Å: Chain C: N.6, I.9, E.10, K.11, V.12, Y.172 No protein-ligand interaction detected (PLIP) PEG.14: 9 residues within 4Å: Chain C: D.33, Y.34, N.36, T.37, D.97, K.124, S.125, K.127, Y.146 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.124 PEG.15: 7 residues within 4Å: Chain B: Y.62 Chain C: D.8, Y.163, K.164, Q.166, Y.167, V.180 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.62 PEG.16: 5 residues within 4Å: Chain B: Q.166 Chain C: V.38, E.64, G.95, R.96 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.95 PEG.19: 6 residues within 4Å: Chain D: N.6, I.9, E.10, K.11, V.12, Y.172 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.10 PEG.20: 8 residues within 4Å: Chain D: D.33, Y.34, T.37, D.97, K.124, S.125, K.127, Y.146 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, B.W. et al., Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction. Elife (2019)

Release Date

2019-05-01

Peptides

Hypoxanthine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Hypoxanthine phosphoribosyltransferase

Related Entries With Identical Sequence