SMTL ID : 4xfj.1

Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

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

ANP.1: 15 residues within 4Å: Chain A: A.16, Y.17, S.18, T.23, V.41, A.42, I.43, Q.47, R.103, I.106, H.124, G.125, C.126, F.136 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.18, A:S.18, A:I.43, A:I.43, A:Q.47, A:G.125, A:G.125 Water bridges: A:G.20, A:L.21, A:D.22, A:D.22, A:R.103, A:R.103, A:G.125, A:D.132, A:D.132, A:D.132 ANP.9: 14 residues within 4Å: Chain B: A.16, Y.17, S.18, T.23, V.41, I.43, Q.47, R.103, I.106, H.124, G.125, C.126, F.136 Ligands: MG.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.18, B:S.18, B:I.43, B:I.43, B:Q.47, B:R.103, B:G.125, B:G.125, B:I.184 Water bridges: B:G.20, B:R.103, B:R.103, B:R.103, B:R.103, B:I.184, B:D.185 ANP.14: 15 residues within 4Å: Chain C: A.16, Y.17, S.18, T.23, V.41, A.42, I.43, Q.47, R.103, I.106, H.124, G.125, C.126, F.136 Ligands: MG.15 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.18, C:S.18, C:I.43, C:I.43, C:Q.47, C:G.125, C:G.125 Water bridges: C:G.20, C:L.21, C:D.22, C:D.22, C:R.103, C:R.103, C:G.125, C:D.132, C:D.132, C:D.132 ANP.22: 14 residues within 4Å: Chain D: A.16, Y.17, S.18, T.23, V.41, I.43, Q.47, R.103, I.106, H.124, G.125, C.126, F.136 Ligands: MG.23 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.18, D:S.18, D:I.43, D:I.43, D:Q.47, D:R.103, D:G.125, D:G.125, D:I.184 Water bridges: D:G.20, D:R.103, D:R.103, D:R.103, D:R.103, D:I.184, D:D.185

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: D.93 Chain B: R.309 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: ANP.14 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain C: D.93 Chain D: R.309 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Ligands: ANP.22 No protein-ligand interaction detected (PLIP)

4 x ARG: ARGININE(Non-covalent)

ARG.3: 13 residues within 4Å: Chain A: Y.95, S.99, A.100, N.131, R.135, S.183, D.185, A.192, E.194, E.268, E.278, Y.280, Y.320 15 PLIP interactions: 14 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:A.100, A:N.131, A:S.183, A:E.194, A:E.268, A:Y.280, A:Y.320, A:Y.320, R.3 Water bridges: A:N.131, A:D.132, A:E.278 Salt bridges: A:R.135, A:E.194, A:E.278 ARG.11: 14 residues within 4Å: Chain B: Y.95, S.99, A.100, N.131, R.135, S.183, D.185, A.192, V.193, E.194, E.268, E.278, Y.280, Y.320 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:Y.280 Hydrogen bonds: B:Y.95, B:Y.95, B:N.131, B:S.183, B:S.183, B:E.268 Water bridges: B:R.103, B:N.131 Salt bridges: B:R.135, B:E.194, B:E.278 ARG.16: 13 residues within 4Å: Chain C: Y.95, S.99, A.100, N.131, R.135, S.183, D.185, A.192, E.194, E.268, E.278, Y.280, Y.320 15 PLIP interactions: 14 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:A.100, C:N.131, C:S.183, C:E.194, C:E.268, C:Y.280, C:Y.320, C:Y.320, R.16 Water bridges: C:N.131, C:D.132, C:E.278 Salt bridges: C:R.135, C:E.194, C:E.278 ARG.24: 14 residues within 4Å: Chain D: Y.95, S.99, A.100, N.131, R.135, S.183, D.185, A.192, V.193, E.194, E.268, E.278, Y.280, Y.320 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:Y.280 Hydrogen bonds: D:Y.95, D:Y.95, D:N.131, D:S.183, D:S.183, D:E.268 Water bridges: D:R.103, D:N.131 Salt bridges: D:R.135, D:E.194, D:E.278

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

EDO.4: 6 residues within 4Å: Chain A: T.380, F.381, D.382, A.385 Chain D: Q.391, L.395 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.380, A:D.382, A:D.382, D:Q.391 EDO.5: 4 residues within 4Å: Chain A: E.199, H.200, L.201 Chain B: Y.368 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.200, A:L.201 Water bridges: A:W.202, A:W.202 EDO.7: 5 residues within 4Å: Chain A: A.401, D.404 Chain B: S.142, L.143, F.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.404 EDO.8: 4 residues within 4Å: Chain A: L.143, F.325 Chain B: A.401, D.404 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.404, B:D.404 EDO.12: 6 residues within 4Å: Chain B: T.380, F.381, D.382, A.385 Chain C: Q.391, L.395 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.380, B:D.382, B:D.382, C:Q.391 EDO.13: 4 residues within 4Å: Chain A: Y.368 Chain B: E.199, H.200, L.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.201 Water bridges: B:W.202 EDO.17: 6 residues within 4Å: Chain B: Q.391, L.395 Chain C: T.380, F.381, D.382, A.385 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Q.391, C:T.380, C:D.382, C:D.382 EDO.18: 4 residues within 4Å: Chain C: E.199, H.200, L.201 Chain D: Y.368 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.200, C:L.201 Water bridges: C:W.202, C:W.202 EDO.20: 5 residues within 4Å: Chain C: A.401, D.404 Chain D: S.142, L.143, F.325 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.404 EDO.21: 4 residues within 4Å: Chain C: L.143, F.325 Chain D: A.401, D.404 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.404, D:D.404 EDO.25: 6 residues within 4Å: Chain A: Q.391, L.395 Chain D: T.380, F.381, D.382, A.385 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.380, D:D.382, D:D.382, A:Q.391 EDO.26: 4 residues within 4Å: Chain C: Y.368 Chain D: E.199, H.200, L.201 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.201 Water bridges: D:W.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine. To Be Published

Release Date

2015-01-14

Peptides

Argininosuccinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Argininosuccinate synthase

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