SMTL ID : 2x75.1

Staphylococcus aureus adenylosuccinate lyase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 5 residues within 4Å: Chain A: Q.259, K.268 Chain D: H.68, S.94 Ligands: AMP.2 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Q.259, D:S.94, D:S.94 Salt bridges: A:K.268, A:K.268, D:H.68 OXL.5: 5 residues within 4Å: Chain B: Q.259, K.268 Chain C: H.68, S.94 Ligands: AMP.6 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.94, C:S.94, B:Q.259 Water bridges: C:T.93 Salt bridges: C:H.68, B:K.268, B:K.268 OXL.9: 5 residues within 4Å: Chain B: H.68, S.94 Chain C: Q.259, K.268 Ligands: AMP.10 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Q.259, B:S.94, B:S.94 Salt bridges: C:K.268, C:K.268, B:H.68 Water bridges: B:T.93 OXL.13: 5 residues within 4Å: Chain A: H.68, S.94 Chain D: Q.259, K.268 Ligands: AMP.14 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:Q.259, A:S.94, A:S.94 Salt bridges: D:K.268, D:K.268, A:H.68

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 16 residues within 4Å: Chain A: R.4, Y.5, N.276 Chain B: H.141 Chain D: R.67, H.68, D.69, S.94, T.95, Q.212, R.301, I.303, S.306, S.307, R.310 Ligands: OXL.1 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:E.63, D:R.67, D:D.69, D:Q.212, A:R.4, A:Y.5, A:Y.5, A:N.276 Water bridges: D:Q.212, A:R.326 Salt bridges: D:R.310, A:R.4 AMP.6: 16 residues within 4Å: Chain A: H.141 Chain B: R.4, Y.5, N.276 Chain C: R.67, H.68, D.69, S.94, T.95, Q.212, R.301, I.303, S.306, S.307, R.310 Ligands: OXL.5 15 PLIP interactions: 1 interactions with chain A, 7 interactions with chain C, 7 interactions with chain B Water bridges: A:T.140, B:R.326 Hydrogen bonds: C:E.63, C:E.63, C:R.67, C:D.69, C:T.95, C:Q.212, B:R.4, B:Y.5, B:Y.5, B:Y.5, B:N.276 Salt bridges: C:R.310, B:R.4 AMP.10: 16 residues within 4Å: Chain B: R.67, H.68, D.69, S.94, T.95, Q.212, R.301, I.303, S.306, S.307, R.310 Chain C: R.4, Y.5, N.276 Chain D: H.141 Ligands: OXL.9 15 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D, 7 interactions with chain C Hydrogen bonds: B:E.63, B:E.63, B:R.67, B:D.69, B:T.95, B:Q.212, C:R.4, C:Y.5, C:Y.5, C:Y.5, C:N.276 Salt bridges: B:R.310, C:R.4 Water bridges: D:T.140, C:R.326 AMP.14: 16 residues within 4Å: Chain A: R.67, H.68, D.69, S.94, T.95, Q.212, R.301, I.303, S.306, S.307, R.310 Chain C: H.141 Chain D: R.4, Y.5, N.276 Ligands: OXL.13 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:R.4, D:Y.5, D:Y.5, D:N.276, A:E.63, A:R.67, A:D.69, A:Q.212 Water bridges: D:R.326, A:Q.212 Salt bridges: D:R.4, A:R.310

4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 4 residues within 4Å: Chain A: A.125, E.126, K.129, N.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.129 P6G.7: 4 residues within 4Å: Chain B: A.125, E.126, K.129, N.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.129 P6G.11: 4 residues within 4Å: Chain C: A.125, E.126, K.129, N.130 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.129 P6G.15: 4 residues within 4Å: Chain D: A.125, E.126, K.129, N.130 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.129

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: A.207, V.209, L.214, Q.215, R.218 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: A.207, V.209, L.214, Q.215, R.218 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: A.207, V.209, L.214, Q.215, R.218 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain D: A.207, V.209, L.214, Q.215, R.218 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fyfe, P.K. et al., Structure of Staphylococcus Aureus Adenylosuccinate Lyase (Purb) and Assessment of its Potential as a Target for Structure-Based Inhibitor Discovery. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-03-09

Peptides

ADENYLOSUCCINATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ADENYLOSUCCINATE LYASE