SMTL ID : 2hcr.1

crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with AMP(ATP), cadmium and sulfate ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.308, V.309, S.310 Chain B: R.104 Chain C: S.47, R.49 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: A.223, D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP SO4.3: 8 residues within 4Å: Chain A: S.132, Q.135, N.144, Y.146 Chain B: K.99, K.100, D.101, K.102 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: R.104 Chain B: S.308, V.309, S.310 Chain F: S.47, R.49 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain B: A.223, D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP SO4.8: 8 residues within 4Å: Chain A: K.99, K.100, D.101, K.102 Chain B: S.132, Q.135, N.144, Y.146 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain C: S.308, V.309, S.310 Chain D: R.104 Chain E: S.47, R.49 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain C: A.223, D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP SO4.13: 8 residues within 4Å: Chain C: S.132, Q.135, N.144, Y.146 Chain D: K.99, K.100, D.101, K.102 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: S.47, R.49 Chain C: R.104 Chain D: S.308, V.309, S.310 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain D: A.223, D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain C: K.99, K.100, D.101, K.102 Chain D: S.132, Q.135, N.144, Y.146 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain A: S.47, R.49 Chain E: S.308, V.309, S.310 Chain F: R.104 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain E: A.223, D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain E: S.132, Q.135, N.144, Y.146 Chain F: K.99, K.100, D.101, K.102 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain D: S.47, R.49 Chain E: R.104 Chain F: S.308, V.309, S.310 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain F: A.223, D.224, T.225, C.226, G.227, T.228 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain E: K.99, K.100, D.101, K.102 Chain F: S.132, Q.135, N.144, Y.146 Ligand excluded by PLIP

6 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: D.171, D.220 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.171, A:D.171 CD.9: 3 residues within 4Å: Chain B: D.171, D.220, D.221 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.171, B:D.171, B:D.220 CD.14: 2 residues within 4Å: Chain C: D.171, D.220 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.171, C:D.171 CD.19: 3 residues within 4Å: Chain D: D.171, D.220, D.221 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.171, D:D.171, D:D.220 CD.24: 2 residues within 4Å: Chain E: D.171, D.220 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.171, E:D.171 CD.29: 3 residues within 4Å: Chain F: D.171, D.220, D.221 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.171, F:D.171, F:D.220

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 9 residues within 4Å: Chain A: R.96, Q.97, K.99, D.101, H.130 Chain B: K.176 Chain F: F.35, N.37, E.39 10 PLIP interactions: 5 interactions with chain A, 4 interactions with chain F, 1 interactions with chain B Hydrogen bonds: A:R.96, A:D.101, F:N.37, F:N.37 Salt bridges: A:K.99, A:H.130, B:K.176 pi-Cation interactions: A:R.96 pi-Stacking: F:F.35, F:F.35 AMP.10: 10 residues within 4Å: Chain A: K.176 Chain B: R.96, Q.97, D.98, K.99, D.101, H.130 Chain C: F.35, N.37, E.39 16 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.97, B:D.101, B:D.224, C:N.37, C:N.37, C:E.39 Water bridges: B:Y.94, B:R.96, B:Q.97, C:E.43 Salt bridges: B:K.99, B:H.130, A:K.176 pi-Cation interactions: B:R.96 pi-Stacking: C:F.35, C:F.35 AMP.15: 9 residues within 4Å: Chain B: F.35, N.37, E.39 Chain C: R.96, Q.97, K.99, D.101, H.130 Chain D: K.176 10 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:R.96, C:D.101, B:N.37, B:N.37 Salt bridges: C:K.99, C:H.130, D:K.176 pi-Cation interactions: C:R.96 pi-Stacking: B:F.35, B:F.35 AMP.20: 10 residues within 4Å: Chain C: K.176 Chain D: R.96, Q.97, D.98, K.99, D.101, H.130 Chain E: F.35, N.37, E.39 16 PLIP interactions: 9 interactions with chain D, 6 interactions with chain E, 1 interactions with chain C Hydrogen bonds: D:Q.97, D:D.101, D:D.224, E:N.37, E:N.37, E:E.39 Water bridges: D:Y.94, D:R.96, D:Q.97, E:E.43 Salt bridges: D:K.99, D:H.130, C:K.176 pi-Cation interactions: D:R.96 pi-Stacking: E:F.35, E:F.35 AMP.25: 9 residues within 4Å: Chain D: F.35, N.37, E.39 Chain E: R.96, Q.97, K.99, D.101, H.130 Chain F: K.176 10 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: E:R.96, E:D.101, D:N.37, D:N.37 Salt bridges: E:K.99, E:H.130, F:K.176 pi-Cation interactions: E:R.96 pi-Stacking: D:F.35, D:F.35 AMP.30: 10 residues within 4Å: Chain A: F.35, N.37, E.39 Chain E: K.176 Chain F: R.96, Q.97, D.98, K.99, D.101, H.130 16 PLIP interactions: 6 interactions with chain A, 9 interactions with chain F, 1 interactions with chain E Hydrogen bonds: A:N.37, A:N.37, A:E.39, F:Q.97, F:D.101, F:D.224 Water bridges: A:E.43, F:Y.94, F:R.96, F:Q.97 pi-Stacking: A:F.35, A:F.35 Salt bridges: F:K.99, F:H.130, E:K.176 pi-Cation interactions: F:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site. Biochem.J. (2007)

Release Date

2006-10-24

Peptides

Ribose-phosphate pyrophosphokinase I: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Ribose-phosphate pyrophosphokinase I

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