SMTL ID : 6w1i.1

Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

8 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: N.30, S.63, D.128, F.129 Ligands: NA.2, G4P.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.30 NA.2: 7 residues within 4Å: Chain A: I.60, S.63, D.127, D.128, F.129 Ligands: NA.1, G4P.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.127 NA.4: 6 residues within 4Å: Chain B: N.30, S.63, D.128, F.129 Ligands: NA.5, G4P.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.30, B:D.128 NA.5: 7 residues within 4Å: Chain B: I.60, S.63, D.127, D.128, F.129 Ligands: NA.4, G4P.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.127 NA.7: 6 residues within 4Å: Chain C: N.30, S.63, D.128, F.129 Ligands: NA.8, G4P.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.30 NA.8: 7 residues within 4Å: Chain C: I.60, S.63, D.127, D.128, F.129 Ligands: NA.7, G4P.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.128 NA.10: 6 residues within 4Å: Chain D: N.30, S.63, D.128, F.129 Ligands: NA.11, G4P.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.30, D:S.63 NA.11: 8 residues within 4Å: Chain D: I.60, S.63, G.64, D.127, D.128, F.129 Ligands: NA.10, G4P.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.127 Water bridges: D:F.129

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

G4P.3: 25 residues within 4Å: Chain A: Q.21, V.22, L.23, K.24, V.25, N.30, E.61, S.62, S.63, K.84, S.101, T.103, K.104, D.128, F.129, A.131, N.132, G.133, K.159, Q.162 Chain B: R.83, L.88, T.89 Ligands: NA.1, NA.2 38 PLIP interactions: 5 interactions with chain B, 33 interactions with chain A Water bridges: B:R.83, B:R.83, B:L.88, B:T.89, A:G.64, A:K.84, A:K.84, A:K.84, A:K.84, A:K.84, A:K.84, A:T.103, A:D.128, A:F.129, A:A.131, A:G.133, A:Q.134, A:Q.134, A:Q.162 Salt bridges: B:R.83, A:K.84, A:K.84 Hydrogen bonds: A:L.23, A:L.23, A:L.23, A:E.61, A:S.62, A:S.63, A:S.63, A:S.101, A:S.101, A:T.103, A:N.132, A:N.132, A:K.159 pi-Stacking: A:F.129, A:F.129 pi-Cation interactions: A:F.129 G4P.6: 24 residues within 4Å: Chain A: R.83, L.88, T.89 Chain B: Q.21, V.22, L.23, K.24, V.25, N.30, E.61, S.62, S.63, K.84, S.101, F.102, T.103, D.128, F.129, A.131, N.132, G.133, K.159 Ligands: NA.4, NA.5 39 PLIP interactions: 35 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:L.23, B:L.23, B:L.23, B:S.62, B:S.63, B:S.63, B:S.101, B:S.101, B:F.102, B:N.132, B:N.132, B:K.159 Water bridges: B:V.25, B:N.30, B:G.64, B:K.84, B:K.84, B:K.84, B:K.84, B:K.84, B:K.84, B:D.127, B:D.128, B:D.128, B:F.129, B:A.131, B:G.133, B:Q.134, B:Q.162, B:Q.162, A:E.61, A:R.83, A:R.83 Salt bridges: B:K.84, B:K.84, A:R.83 pi-Stacking: B:F.129, B:F.129 pi-Cation interactions: B:F.129 G4P.9: 24 residues within 4Å: Chain C: V.22, L.23, K.24, V.25, N.30, E.61, S.62, S.63, K.84, Y.100, S.101, F.102, T.103, D.128, F.129, A.131, N.132, G.133, K.159 Chain D: R.83, L.88, T.89 Ligands: NA.7, NA.8 35 PLIP interactions: 32 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:L.23, C:L.23, C:L.23, C:S.62, C:S.63, C:S.63, C:S.101, C:F.102, C:T.103, C:D.128, C:N.132, C:N.132, C:G.133, C:K.159 Water bridges: C:V.25, C:E.61, C:G.64, C:K.84, C:K.84, C:K.84, C:K.84, C:K.84, C:K.84, C:D.127, C:A.131, C:Q.134, C:Q.162, D:R.83, D:R.83 Salt bridges: C:K.84, C:K.84, D:R.83 pi-Stacking: C:F.129, C:F.129 pi-Cation interactions: C:F.129 G4P.12: 24 residues within 4Å: Chain C: R.83, L.88, T.89 Chain D: Q.21, V.22, L.23, K.24, V.25, N.30, E.61, S.62, S.63, K.84, S.101, F.102, T.103, D.128, F.129, A.131, N.132, G.133, K.159 Ligands: NA.10, NA.11 33 PLIP interactions: 29 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:L.23, D:L.23, D:L.23, D:N.30, D:E.61, D:S.62, D:S.63, D:S.63, D:F.102, D:T.103, D:D.128, D:N.132, D:N.132, D:K.159 Water bridges: D:V.25, D:G.64, D:K.84, D:K.84, D:D.127, D:D.128, D:F.129, D:A.131, D:Q.134, D:Q.162, C:R.83, C:R.83, C:R.83 Salt bridges: D:K.84, D:K.84, C:R.83 pi-Stacking: D:F.129, D:F.129 pi-Cation interactions: D:F.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, B.W. et al., Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp. J.Mol.Biol. (2020)

Release Date

2020-07-29

Peptides

Xanthine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Xanthine phosphoribosyltransferase

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