SMTL ID : 3nvs.1

1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.02 Å

Oligo State

monomer

Ligands

1 x S3P: SHIKIMATE-3-PHOSPHATE(Non-covalent)

S3P.1: 15 residues within 4Å: Chain A: K.46, S.47, R.51, T.121, S.194, S.195, Q.196, S.222, Y.225, D.338, N.361, K.365 Ligands: SKM.2, GPJ.3, PO4.12 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Q.196, A:Y.225, A:Y.225, A:Y.225 Hydrogen bonds: A:S.194, A:S.195, A:Q.196, A:Q.196, A:S.222, A:S.222, A:D.338, A:N.361, A:K.365 Water bridges: A:S.194, A:S.194, A:D.338 Salt bridges: A:R.51, A:K.365

1 x SKM: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID(Non-covalent)

SKM.2: 11 residues within 4Å: Chain A: K.46, S.47, R.51, T.121, Q.196, Y.225, D.338, K.365 Ligands: S3P.1, GPJ.3, PO4.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.225, A:Y.225, A:Y.225 Hydrogen bonds: A:Q.196, A:D.338, A:K.365, A:K.365 Water bridges: A:S.194, A:D.338 Salt bridges: A:R.51

1 x GPJ: GLYPHOSATE(Non-covalent)

GPJ.3: 16 residues within 4Å: Chain A: K.46, N.118, A.119, G.120, T.121, R.124, R.148, Q.196, D.338, E.366, R.369, H.410, R.411, K.436 Ligands: S3P.1, SKM.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.46, A:K.46, A:G.120, A:R.148, A:R.148, A:Q.196, A:Q.196, A:K.436 Water bridges: A:K.46, A:T.121, A:R.124 Salt bridges: A:K.46, A:R.369, A:H.410, A:R.411

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

MG.4: 2 residues within 4Å: Chain A: E.147, Q.169 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.147, H2O.17, H2O.18, H2O.19, H2O.24 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain A: R.378, T.383, V.384 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: V.40, N.41, K.444, Q.447 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: A.402, A.403 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: R.378, V.384, E.385, E.386 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 5 residues within 4Å: Chain A: K.292, I.299, Q.300, D.303, W.314 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.303, A:W.314 Water bridges: A:K.292, A:W.314 Salt bridges: A:K.292, A:D.303

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 10 residues within 4Å: Chain A: I.193, S.194, S.195, Q.196, V.221, S.222, N.361, K.365 Ligands: S3P.1, SKM.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:S.195, A:Q.196, A:S.222, A:N.361 Water bridges: A:S.194 Salt bridges: A:K.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1-Carboxyvinyltransferase from Vibrio cholerae in complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate. TO BE PUBLISHED

Release Date

2010-07-21

Peptides

3-phosphoshikimate 1-carboxyvinyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-phosphoshikimate 1-carboxyvinyltransferase