SMTL ID : 3dah.1 (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-trimer

Ligands

7 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: 5 residues within 4Å: Chain A: R.109 Chain B: D.310, S.311, V.312, M.313 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.310, B:V.312, B:M.313 Salt bridges: A:R.109 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: 2 residues within 4Å: Chain B: R.53 Chain C: R.109 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Salt bridges: C:R.109, B:R.53 Hydrogen bonds: B:N.51 Water bridges: B:R.53 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

3 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 3 residues within 4Å: Chain A: R.100, Q.101, H.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.100 Water bridges: A:Y.98, A:R.100, A:R.103 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: 5 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Q.101, C:D.41 Water bridges: B:Y.98, C:S.40 Salt bridges: B:R.103, B:H.135 pi-Cation interactions: B:R.100 pi-Stacking: C:F.39, C: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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ribose-phosphate pyrophosphokinase

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