SMTL ID : 7k5z.1

Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1 in complex with ANPPNP and a substrate analogue Arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 20 residues within 4Å: Chain A: A.19, Y.20, S.21, G.23, D.25, T.26, V.45, I.46, C.47, L.49, Q.51, R.105, I.108, H.126, G.127, A.128, F.138, R.187 Ligands: ARG.2, MG.3 20 PLIP interactions: 17 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:S.21, A:C.47, A:C.47, A:Q.51, A:R.105, A:G.127, A:G.127 Water bridges: A:G.23, A:L.24, A:T.26, A:R.105, A:R.105, A:R.187, A:R.187, A:R.187, A:R.187, A:R.187, R.2, R.2 Salt bridges: R.2 ANP.11: 17 residues within 4Å: Chain B: A.19, Y.20, S.21, T.26, V.45, I.46, C.47, L.49, Q.51, R.105, I.108, H.126, G.127, A.128, F.138 Ligands: ARG.12, MG.13 18 PLIP interactions: 14 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: B:S.21, B:C.47, B:C.47, B:Q.51, B:R.105, B:G.127, B:G.127 Water bridges: B:G.23, B:G.23, B:D.25, B:D.25, B:R.105, B:R.105, B:R.187, R.12, R.12, R.12 Salt bridges: R.12 ANP.19: 17 residues within 4Å: Chain C: A.19, Y.20, S.21, D.25, T.26, V.45, I.46, C.47, Q.51, R.105, I.108, H.126, G.127, A.128, F.138 Ligands: ARG.20, MG.21 17 PLIP interactions: 13 interactions with chain C, 4 Ligand-Ligand interactions Hydrogen bonds: C:S.21, C:C.47, C:C.47, C:Q.51, C:R.105, C:G.127, C:G.127 Water bridges: C:G.23, C:D.25, C:R.105, C:R.105, C:R.187, C:R.187, R.20, R.20, R.20 Salt bridges: R.20 ANP.28: 18 residues within 4Å: Chain D: A.19, Y.20, S.21, D.25, T.26, V.45, I.46, C.47, L.49, Q.51, R.105, I.108, H.126, G.127, A.128, F.138 Ligands: ARG.29, MG.30 19 PLIP interactions: 16 interactions with chain D, 3 Ligand-Ligand interactions Hydrogen bonds: D:S.21, D:C.47, D:C.47, D:Q.51, D:G.127, D:G.127 Water bridges: D:G.23, D:G.23, D:L.24, D:L.24, D:R.105, D:R.105, D:R.187, D:R.187, D:R.187, R.29, R.29 Salt bridges: D:R.105, R.29

4 x ARG: ARGININE(Non-covalent)

ARG.2: 15 residues within 4Å: Chain A: Y.98, T.102, R.105, N.133, D.134, R.137, S.186, R.187, Y.193, S.195, E.197, E.271, Y.283, Y.323 Ligands: ANP.1 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.102, A:Y.283 Hydrogen bonds: A:Y.98, A:Y.98, A:R.105, A:N.133, A:S.186, A:E.271 Water bridges: A:N.133, A:D.134, A:R.187, A:D.188, A:D.188, R.2 Salt bridges: A:D.134, A:R.137, A:D.188, A:E.197 ARG.12: 16 residues within 4Å: Chain B: Y.98, T.102, R.105, N.133, D.134, R.137, S.186, R.187, D.188, Y.193, S.195, E.197, E.271, Y.283, Y.323 Ligands: ANP.11 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:T.102, B:Y.283 Hydrogen bonds: B:Y.98, B:Y.98, B:R.105, B:N.133, B:S.186, B:E.271 Water bridges: B:D.134, B:D.134, B:R.187, B:R.187 Salt bridges: B:D.134, B:R.137, B:D.188, B:E.197 ARG.20: 16 residues within 4Å: Chain C: Y.98, T.102, R.105, N.133, D.134, R.137, S.186, R.187, D.188, Y.193, S.195, E.197, E.271, Y.283, Y.323 Ligands: ANP.19 16 PLIP interactions: 13 interactions with chain C, 3 Ligand-Ligand interactions Hydrophobic interactions: C:T.102, C:Y.283 Hydrogen bonds: C:T.102, C:R.105, C:N.133, C:S.186, C:E.271, C:Y.323, R.20, R.20 Water bridges: C:R.187, R.20 Salt bridges: C:D.134, C:R.137, C:D.188, C:E.197 ARG.29: 16 residues within 4Å: Chain D: Y.98, T.102, R.105, N.133, D.134, R.137, S.186, R.187, D.188, Y.193, S.195, E.197, E.271, Y.283, Y.323 Ligands: ANP.28 18 PLIP interactions: 15 interactions with chain D, 3 Ligand-Ligand interactions Hydrophobic interactions: D:T.102, D:Y.283 Hydrogen bonds: D:T.102, D:R.105, D:N.133, D:S.186, D:E.271, D:Y.283, D:Y.323, R.29, R.29 Water bridges: D:D.134, D:R.187, R.29 Salt bridges: D:D.134, D:R.137, D:D.188, D:E.197

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ANP.11 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Ligands: ANP.19 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Ligands: ANP.28 No protein-ligand interaction detected (PLIP)

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

EDO.4: 3 residues within 4Å: Chain A: Y.71, V.72 Ligands: EDO.5 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: K.69, A.70, Y.71 Ligands: EDO.4 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: H.365, S.366, P.367 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: Q.405, Q.408 Chain B: P.147, Q.148 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: P.147, Q.148 Chain B: Q.405 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: T.304, R.305, S.306 Chain C: S.399, A.400 Chain D: Y.140 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: K.59, K.69, A.70, Y.71 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: H.365, S.366, P.367 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: Q.110, V.113, E.114, L.145 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: T.304, R.305, S.306 Chain C: Y.140 Chain D: S.399, A.400 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: S.399, A.400 Chain B: Y.140 Chain C: T.304, R.305, S.306 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: A.70, Y.71, V.72 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain C: A.70 Ligands: EDO.22 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain C: H.365, S.366, P.367 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: Q.405 Chain D: P.147, Q.148 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: P.147, Q.148 Chain D: Q.405 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: Y.140 Chain B: S.399, A.400 Chain D: T.304, R.305, S.306 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain D: K.59, K.69, A.70, Y.71 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain D: H.365, S.366, P.367 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: L.314, T.317 Chain D: L.310, S.313 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: D.232, K.234, V.239, A.240, E.245 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.232 Salt bridges: A:K.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J.A. et al., Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1 in complex with ANPPNP and a substrate analogue Arginine. to be published

Release Date

2020-09-30

Peptides

Argininosuccinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Argininosuccinate synthase

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