SMTL ID : 3dah.2 (1 other biounit)

2.3 A crystal structure of ribose-phosphate pyrophosphokinase from Burkholderia pseudomallei

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: S.311, V.312, M.313 Chain B: R.109 Chain C: N.51, R.53 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Water bridges: C:V.52 Salt bridges: C:R.53, B:R.109 Hydrogen bonds: A:V.312, A:M.313 PO4.2: 7 residues within 4Å: Chain A: V.226, D.227, T.228, A.229, G.230, T.231, L.232 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.227, A:T.228, A:T.228, A:T.228, A:A.229, A:G.230, A:T.231, A:T.231, A:T.231, A:L.232 PO4.4: 7 residues within 4Å: Chain A: R.109 Chain B: D.310, S.311, V.312, M.313 Chain D: N.51, R.53 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:D.310, B:V.312, B:M.313 Salt bridges: A:R.109, D:R.53 Water bridges: D:R.53 PO4.5: 7 residues within 4Å: Chain B: V.226, D.227, T.228, A.229, G.230, T.231, L.232 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.227, B:T.228, B:T.228, B:A.229, B:G.230, B:T.231, B:T.231, B:L.232 PO4.6: 3 residues within 4Å: Chain B: R.53 Chain C: R.109 Chain F: R.305 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: B:N.51 Water bridges: B:R.53 Salt bridges: B:R.53, C:R.109, F:R.305 PO4.7: 1 residues within 4Å: Chain B: R.263 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.263 PO4.10: 6 residues within 4Å: Chain C: V.226, D.227, T.228, A.229, G.230, T.231 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.227, C:D.227, C:D.227, C:T.228, C:T.228, C:A.229, C:G.230, C:T.231 PO4.11: 6 residues within 4Å: Chain D: S.311, V.312, M.313 Chain E: R.109 Chain F: N.51, R.53 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D, 2 interactions with chain F Salt bridges: E:R.109, F:R.53 Hydrogen bonds: D:V.312, D:M.313 Water bridges: F:V.52 PO4.12: 7 residues within 4Å: Chain D: V.226, D.227, T.228, A.229, G.230, T.231, L.232 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.227, D:T.228, D:T.228, D:T.228, D:A.229, D:G.230, D:T.231, D:T.231, D:T.231, D:L.232 PO4.14: 7 residues within 4Å: Chain A: N.51, R.53 Chain D: R.109 Chain E: D.310, S.311, V.312, M.313 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 3 interactions with chain E Water bridges: A:R.53 Salt bridges: A:R.53, D:R.109 Hydrogen bonds: E:D.310, E:V.312, E:M.313 PO4.15: 7 residues within 4Å: Chain E: V.226, D.227, T.228, A.229, G.230, T.231, L.232 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.227, E:T.228, E:T.228, E:A.229, E:G.230, E:T.231, E:T.231, E:L.232 PO4.16: 3 residues within 4Å: Chain C: R.305 Chain E: R.53 Chain F: R.109 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E, 1 interactions with chain C Salt bridges: F:R.109, E:R.53, C:R.305 Hydrogen bonds: E:N.51 Water bridges: E:R.53 PO4.17: 1 residues within 4Å: Chain E: R.263 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.263 PO4.20: 6 residues within 4Å: Chain F: V.226, D.227, T.228, A.229, G.230, T.231 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:D.227, F:D.227, F:D.227, F:T.228, F:T.228, F:A.229, F:G.230, F:T.231

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 6 residues within 4Å: Chain A: R.100, Q.101, H.135 Chain D: F.39, D.41, E.43 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:D.41, D:E.43, A:R.100 Water bridges: D:S.40, D:S.40, A:Y.98, A:R.103 pi-Stacking: D:F.39, D:F.39 Salt bridges: A:H.135 AMP.8: 8 residues within 4Å: Chain B: F.39, D.41, E.43 Chain C: R.100, Q.101, R.103, P.105, H.135 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:D.41, B:E.43 pi-Stacking: B:F.39, B:F.39 Water bridges: C:Y.98, C:R.100 Salt bridges: C:R.103, C:H.135 AMP.9: 7 residues within 4Å: Chain B: R.100, Q.101, R.103, H.135 Chain C: F.39, D.41, E.43 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:D.41, B:Q.101 Water bridges: C:S.40, B:Y.98 pi-Stacking: C:F.39, C:F.39 Salt bridges: B:R.103, B:H.135 pi-Cation interactions: B:R.100 AMP.13: 6 residues within 4Å: Chain A: F.39, D.41, E.43 Chain D: R.100, Q.101, H.135 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:R.100, A:D.41, A:E.43 Water bridges: D:Y.98, D:R.103, A:S.40, A:S.40 Salt bridges: D:H.135 pi-Stacking: A:F.39, A:F.39 AMP.18: 8 residues within 4Å: Chain E: F.39, D.41, E.43 Chain F: R.100, Q.101, R.103, P.105, H.135 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain E Water bridges: F:Y.98, F:R.100 Salt bridges: F:R.103, F:H.135 Hydrogen bonds: E:D.41, E:E.43 pi-Stacking: E:F.39, E:F.39 AMP.19: 7 residues within 4Å: Chain E: R.100, Q.101, R.103, H.135 Chain F: F.39, D.41, E.43 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:Q.101, F:D.41 Water bridges: E:Y.98, F:S.40 Salt bridges: E:R.103, E:H.135 pi-Cation interactions: E:R.100 pi-Stacking: F:F.39, F:F.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

Release Date

2008-06-10

Peptides

Ribose-phosphate pyrophosphokinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Ribose-phosphate pyrophosphokinase

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