SMTL ID : 5u99.1

Transition state analysis of adenosine triphosphate phosphoribosyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: V.158, G.159, S.160, G.161, R.162, T.163 Ligands: SO4.3, ATP.6 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: G.140, A.141 Chain E: N.10, K.11, R.51 Ligands: SO4.3 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: E.143, D.156, V.157, T.163 Ligands: SO4.1, SO4.2, ATP.6 Ligand excluded by PLIP SO4.7: 8 residues within 4Å: Chain B: V.158, G.159, S.160, G.161, R.162, T.163 Ligands: SO4.9, ATP.12 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain B: G.140, A.141 Chain D: N.10, K.11, R.51 Ligands: SO4.9 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain B: E.143, D.156, V.157, T.163 Ligands: SO4.7, SO4.8, ATP.12 Ligand excluded by PLIP SO4.13: 8 residues within 4Å: Chain C: V.158, G.159, S.160, G.161, R.162, T.163 Ligands: SO4.15, ATP.18 Ligand excluded by PLIP SO4.14: 6 residues within 4Å: Chain C: G.140, A.141 Chain F: N.10, K.11, R.51 Ligands: SO4.15 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain C: E.143, D.156, V.157, T.163 Ligands: SO4.13, SO4.14, ATP.18 Ligand excluded by PLIP SO4.19: 8 residues within 4Å: Chain D: V.158, G.159, S.160, G.161, R.162, T.163 Ligands: SO4.21, ATP.24 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain B: N.10, K.11, R.51 Chain D: G.140, A.141 Ligands: SO4.21 Ligand excluded by PLIP SO4.21: 7 residues within 4Å: Chain D: E.143, D.156, V.157, T.163 Ligands: SO4.19, SO4.20, ATP.24 Ligand excluded by PLIP SO4.25: 8 residues within 4Å: Chain E: V.158, G.159, S.160, G.161, R.162, T.163 Ligands: SO4.27, ATP.30 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain A: N.10, K.11, R.51 Chain E: G.140, A.141 Ligands: SO4.27 Ligand excluded by PLIP SO4.27: 7 residues within 4Å: Chain E: E.143, D.156, V.157, T.163 Ligands: SO4.25, SO4.26, ATP.30 Ligand excluded by PLIP SO4.31: 8 residues within 4Å: Chain F: V.158, G.159, S.160, G.161, R.162, T.163 Ligands: SO4.33, ATP.36 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain C: N.10, K.11, R.51 Chain F: G.140, A.141 Ligands: SO4.33 Ligand excluded by PLIP SO4.33: 7 residues within 4Å: Chain F: E.143, D.156, V.157, T.163 Ligands: SO4.31, SO4.32, ATP.36 Ligand excluded by PLIP

12 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 1 residues within 4Å: Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Ligands: ATP.6, MG.29, ATP.30 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Ligands: ATP.12, MG.23, ATP.24 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: ATP.18 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Ligands: ATP.18, MG.35, ATP.36 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: ATP.24 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Ligands: MG.11, ATP.12, ATP.24 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Ligands: ATP.30 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Ligands: MG.5, ATP.6, ATP.30 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Ligands: ATP.36 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Ligands: MG.17, ATP.18, ATP.36 No protein-ligand interaction detected (PLIP)

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

ATP.6: 19 residues within 4Å: Chain A: G.12, A.13, L.14, R.51, P.52, G.70, D.72, G.90, S.92, Y.118, V.157 Chain E: K.11, R.51 Ligands: SO4.1, SO4.3, MG.4, MG.5, MG.29, ATP.30 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain E Hydrogen bonds: A:A.13, A:D.72, A:S.92, A:S.179 Water bridges: A:K.11, A:L.14, A:R.51, A:K.53, A:K.53, A:Y.118, A:Y.118, E:K.11, E:K.11, E:K.11, E:K.11, E:R.51, E:R.51, E:D.139 Salt bridges: A:R.51, A:R.51, E:K.11, E:R.51 ATP.12: 19 residues within 4Å: Chain B: G.12, A.13, L.14, R.51, P.52, G.70, D.72, G.90, S.92, Y.118, V.157 Chain D: K.11, R.51 Ligands: SO4.7, SO4.9, MG.10, MG.11, MG.23, ATP.24 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain D Hydrogen bonds: B:A.13, B:D.72, B:S.92, B:S.179 Water bridges: B:K.11, B:L.14, B:R.51, B:K.53, B:K.53, B:Y.118, B:Y.118, D:K.11, D:K.11, D:K.11, D:K.11, D:R.51, D:R.51, D:D.139 Salt bridges: B:R.51, B:R.51, D:K.11, D:R.51 ATP.18: 19 residues within 4Å: Chain C: G.12, A.13, L.14, R.51, P.52, G.70, D.72, G.90, S.92, Y.118, V.157 Chain F: K.11, R.51 Ligands: SO4.13, SO4.15, MG.16, MG.17, MG.35, ATP.36 22 PLIP interactions: 13 interactions with chain C, 9 interactions with chain F Hydrogen bonds: C:A.13, C:D.72, C:S.92, C:S.179 Water bridges: C:K.11, C:L.14, C:R.51, C:K.53, C:K.53, C:Y.118, C:Y.118, F:K.11, F:K.11, F:K.11, F:K.11, F:R.51, F:R.51, F:D.139 Salt bridges: C:R.51, C:R.51, F:K.11, F:R.51 ATP.24: 19 residues within 4Å: Chain B: K.11, R.51 Chain D: G.12, A.13, L.14, R.51, P.52, G.70, D.72, G.90, S.92, Y.118, V.157 Ligands: MG.11, ATP.12, SO4.19, SO4.21, MG.22, MG.23 20 PLIP interactions: 11 interactions with chain D, 9 interactions with chain B Hydrogen bonds: D:A.13, D:D.72, D:S.92, D:S.179 Water bridges: D:K.11, D:L.14, D:R.51, D:K.53, D:K.53, B:K.11, B:K.11, B:K.11, B:K.11, B:R.51, B:R.51, B:D.139 Salt bridges: D:R.51, D:R.51, B:K.11, B:R.51 ATP.30: 19 residues within 4Å: Chain A: K.11, R.51 Chain E: G.12, A.13, L.14, R.51, P.52, G.70, D.72, G.90, S.92, Y.118, V.157 Ligands: MG.5, ATP.6, SO4.25, SO4.27, MG.28, MG.29 20 PLIP interactions: 11 interactions with chain E, 9 interactions with chain A Hydrogen bonds: E:A.13, E:D.72, E:S.92, E:S.179 Water bridges: E:K.11, E:L.14, E:R.51, E:K.53, E:K.53, A:K.11, A:K.11, A:K.11, A:K.11, A:R.51, A:R.51, A:D.139 Salt bridges: E:R.51, E:R.51, A:K.11, A:R.51 ATP.36: 19 residues within 4Å: Chain C: K.11, R.51 Chain F: G.12, A.13, L.14, R.51, P.52, G.70, D.72, G.90, S.92, Y.118, V.157 Ligands: MG.17, ATP.18, SO4.31, SO4.33, MG.34, MG.35 20 PLIP interactions: 11 interactions with chain F, 9 interactions with chain C Hydrogen bonds: F:A.13, F:D.72, F:S.92, F:S.179 Water bridges: F:K.11, F:L.14, F:R.51, F:K.53, F:K.53, C:K.11, C:K.11, C:K.11, C:K.11, C:R.51, C:R.51, C:D.139 Salt bridges: F:R.51, F:R.51, C:K.11, C:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moggre, G.J. et al., Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase. ACS Chem. Biol. (2017)

Release Date

2017-09-20

Peptides

ATP phosphoribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

ATP phosphoribosyltransferase