SMTL ID : 7dah.1

Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-hexamer

Ligands

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

PEG.1: 2 residues within 4Å: Chain A: F.200, E.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.201 PEG.10: 2 residues within 4Å: Chain C: F.200, E.201 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.201

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: E.126, D.132, K.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.132, A:K.136 EDO.3: 6 residues within 4Å: Chain A: D.68, G.71, L.72, D.75, R.95 Chain B: M.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68 EDO.9: 3 residues within 4Å: Chain B: R.92, E.103, F.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.92, B:F.104, B:F.104 EDO.11: 3 residues within 4Å: Chain C: L.107, Q.208, A.218 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.208 EDO.13: 6 residues within 4Å: Chain C: I.121, E.126, D.132, L.133, K.136, D.176 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain C: D.68, G.71, L.72, D.75, R.95 Chain D: M.161 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.68, C:D.75 EDO.17: 3 residues within 4Å: Chain A: Y.239 Chain D: M.241, H.277 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.277 EDO.20: 5 residues within 4Å: Chain F: D.67, E.90, T.91, T.141, Y.142 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.67, F:T.141

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 6 residues within 4Å: Chain A: V.182, S.183, T.184, G.185, A.186, T.187 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.183, A:T.184, A:T.184, A:G.185, A:A.186, A:T.187, A:T.187, A:T.187 PO4.15: 6 residues within 4Å: Chain C: V.182, S.183, T.184, G.185, A.186, T.187 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.183, C:T.184, C:T.184, C:G.185, C:A.186, C:T.187, C:T.187

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: C.160, M.161 Chain B: D.68, G.71, L.72, D.75 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.161, B:G.71, B:D.75 GOL.12: 6 residues within 4Å: Chain C: C.160, M.161 Chain D: D.68, G.71, L.72, D.75 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:M.161, D:D.68

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: D.66, D.67, V.87 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.66, B:D.66, B:D.67 MG.16: 3 residues within 4Å: Chain D: D.66, D.67 Ligands: ATP.19 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.66, D:D.67

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.7: 17 residues within 4Å: Chain B: Q.23, K.25, G.26, R.27, R.65, D.66, D.67, G.84, N.86, V.87, G.113, G.114, C.115, L.181, S.183, S.202 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.23, B:K.25, B:R.27, B:D.66, B:D.66, B:D.67, B:N.86, B:N.86, B:Y.142, B:S.183, B:S.183, B:S.202 Water bridges: B:D.66, B:D.66, B:G.84 Salt bridges: B:R.27, B:R.65 pi-Cation interactions: B:R.27, B:R.27 ATP.19: 19 residues within 4Å: Chain D: Q.23, K.25, G.26, R.27, L.28, R.65, D.66, D.67, G.84, N.86, V.87, G.113, G.114, C.115, L.181, S.183, S.202 Ligands: MG.16, PRP.18 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.66, D:D.66, D:D.66, D:N.86, D:N.86, D:S.183, D:S.183, D:S.202 Salt bridges: D:R.27, D:R.65 pi-Cation interactions: D:R.27, D:R.27

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.8: 13 residues within 4Å: Chain A: K.24, R.65 Chain B: G.164, S.165, E.167, D.180, L.181, V.182, S.183, T.184, G.185, A.186, T.187 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Salt bridges: A:R.65 Hydrogen bonds: B:S.165, B:L.181, B:S.183, B:T.184, B:G.185, B:A.186, B:T.187, B:T.187 PRP.18: 14 residues within 4Å: Chain C: K.24, R.65 Chain D: G.164, S.165, E.167, D.180, L.181, V.182, S.183, T.184, G.185, A.186, T.187 Ligands: ATP.19 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.165, D:E.167, D:S.183, D:T.184, D:G.185, D:A.186, D:T.187, D:T.187, D:T.187 Salt bridges: C:R.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pal, R.K. et al., Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP. To Be Published

Release Date

2021-10-20

Peptides

ATP phosphoribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
F

E
B

F
E

ATP phosphoribosyltransferase

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