SMTL ID : 6e5y.2 (1 other biounit)

1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: A.20, F.21, S.22, T.27, Y.44, T.45, A.46, L.48, Q.50, R.110, L.117, F.143, D.197 Ligands: SO4.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.46, A:A.46, A:R.110 Water bridges: A:A.20, A:Q.50, A:Q.50, A:R.110, A:R.110, A:T.113, A:D.139, A:D.139 Salt bridges: A:R.110 AMP.12: 14 residues within 4Å: Chain B: A.20, F.21, S.22, T.27, Y.44, T.45, A.46, L.48, Q.50, R.110, L.117, F.143, D.197 Ligands: SO4.18 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.46, B:A.46, B:R.110 Water bridges: B:A.20, B:Q.50, B:Q.50, B:R.110, B:R.110, B:T.113, B:D.139, B:D.139 Salt bridges: B:R.110 AMP.23: 14 residues within 4Å: Chain C: A.20, F.21, S.22, T.27, Y.44, T.45, A.46, L.48, Q.50, R.110, L.117, F.143, D.197 Ligands: SO4.29 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:A.46, C:A.46, C:R.110 Water bridges: C:A.20, C:Q.50, C:Q.50, C:R.110, C:R.110 Salt bridges: C:R.110 AMP.34: 14 residues within 4Å: Chain D: A.20, F.21, S.22, T.27, Y.44, T.45, A.46, L.48, Q.50, R.110, L.117, F.143, D.197 Ligands: SO4.40 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.46, D:A.46, D:R.110 Water bridges: D:A.20, D:Q.50, D:Q.50, D:R.110, D:R.110 Salt bridges: D:R.110

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

CL.2: 3 residues within 4Å: Chain A: R.243, S.380, A.381 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: G.109, R.110, D.197, N.199 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.134, K.136, G.137, R.285 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: N.284, R.332 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: R.243, S.380, A.381 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: G.109, R.110, D.197, N.199 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: T.134, K.136, G.137, R.285 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: N.284, R.332 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: R.243, S.380, A.381 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: G.109, R.110, D.197, N.199 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: T.134, K.136, G.137, R.285 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: N.284, R.332 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain D: R.243, S.380, A.381 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain D: G.109, R.110, D.197, N.199 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain D: T.134, K.136, G.137, R.285 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain D: N.284, R.332 Ligand excluded by PLIP

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

SO4.6: 6 residues within 4Å: Chain A: G.24, L.25, R.172, Y.186, M.188, S.189 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.25, A:Y.186, A:S.189, A:S.189 Water bridges: A:D.26 Salt bridges: A:R.172 SO4.7: 6 residues within 4Å: Chain A: S.22, G.24, L.25, D.26, T.27 Ligands: AMP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.22, A:G.24, A:D.26, A:T.27, A:T.27 Water bridges: A:L.25 SO4.8: 3 residues within 4Å: Chain A: K.192, S.195, T.196 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.195, A:T.196 Water bridges: A:K.192, A:K.192, A:K.192 Salt bridges: A:K.192 SO4.17: 6 residues within 4Å: Chain B: G.24, L.25, R.172, Y.186, M.188, S.189 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.25, B:Y.186, B:S.189, B:S.189 Water bridges: B:D.26 Salt bridges: B:R.172 SO4.18: 6 residues within 4Å: Chain B: S.22, G.24, L.25, D.26, T.27 Ligands: AMP.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.22, B:G.24, B:D.26, B:T.27, B:T.27 Water bridges: B:L.25 SO4.19: 3 residues within 4Å: Chain B: K.192, S.195, T.196 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.195, B:T.196 Water bridges: B:K.192, B:K.192, B:K.192 Salt bridges: B:K.192 SO4.28: 6 residues within 4Å: Chain C: G.24, L.25, R.172, Y.186, M.188, S.189 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.25, C:S.189, C:S.189 Water bridges: C:D.26 Salt bridges: C:R.172 SO4.29: 6 residues within 4Å: Chain C: S.22, G.24, L.25, D.26, T.27 Ligands: AMP.23 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.22, C:G.24, C:D.26, C:T.27, C:T.27 Water bridges: C:L.25 SO4.30: 3 residues within 4Å: Chain C: K.192, S.195, T.196 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.195, C:T.196 Water bridges: C:K.192, C:K.192, C:K.192 Salt bridges: C:K.192 SO4.39: 6 residues within 4Å: Chain D: G.24, L.25, R.172, Y.186, M.188, S.189 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.25, D:S.189, D:S.189 Water bridges: D:D.26 Salt bridges: D:R.172 SO4.40: 6 residues within 4Å: Chain D: S.22, G.24, L.25, D.26, T.27 Ligands: AMP.34 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.22, D:G.24, D:D.26, D:T.27, D:T.27 Water bridges: D:L.25 SO4.41: 3 residues within 4Å: Chain D: K.192, S.195, T.196 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.195, D:T.196 Water bridges: D:K.192, D:K.192, D:K.192 Salt bridges: D:K.192

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 5 residues within 4Å: Chain A: D.26, A.30, G.130, G.132, P.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.130, A:G.132 Water bridges: A:D.131 EDO.10: 3 residues within 4Å: Chain A: L.73, V.74, D.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.75 Water bridges: A:D.75 EDO.20: 5 residues within 4Å: Chain B: D.26, A.30, G.130, G.132, P.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.130, B:G.132 Water bridges: B:D.131 EDO.21: 3 residues within 4Å: Chain B: L.73, V.74, D.75 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.75 Water bridges: B:D.75 EDO.31: 5 residues within 4Å: Chain C: D.26, A.30, G.130, G.132, P.159 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.130, C:G.132 EDO.32: 3 residues within 4Å: Chain C: L.73, V.74, D.75 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.75 Water bridges: C:D.75, C:D.75 EDO.42: 5 residues within 4Å: Chain D: D.26, A.30, G.130, G.132, P.159 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.130, D:G.132 EDO.43: 3 residues within 4Å: Chain D: L.73, V.74, D.75 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.75 Water bridges: D:D.75, D:D.75

4 x MLA: MALONIC ACID(Non-covalent)

MLA.11: 8 residues within 4Å: Chain A: Y.102, T.106, P.107, N.138, R.142, E.283, Y.295, Y.335 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.138 Water bridges: A:N.138, A:R.142, A:E.283, A:Y.335 Salt bridges: A:R.142, A:R.142 MLA.22: 8 residues within 4Å: Chain B: Y.102, T.106, P.107, N.138, R.142, E.283, Y.295, Y.335 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.138 Water bridges: B:N.138, B:R.142, B:E.283, B:Y.335 Salt bridges: B:R.142, B:R.142 MLA.33: 8 residues within 4Å: Chain C: Y.102, T.106, P.107, N.138, R.142, E.283, Y.295, Y.335 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.102, C:N.138, C:Y.295 Water bridges: C:N.138, C:R.142, C:R.285 Salt bridges: C:R.142, C:R.142 MLA.44: 8 residues within 4Å: Chain D: Y.102, T.106, P.107, N.138, R.142, E.283, Y.295, Y.335 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.102, D:N.138, D:Y.295 Water bridges: D:N.138, D:R.142, D:R.285 Salt bridges: D:R.142, D:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP. To Be Published

Release Date

2018-08-01

Peptides

Argininosuccinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Argininosuccinate synthase

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