SMTL ID : 1e4e.1

D-alanyl-D-lacate ligase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 22 residues within 4Å: Chain A: K.133, F.169, K.171, S.175, G.176, S.177, S.178, V.181, E.207, Q.208, A.209, V.210, E.214, L.236, I.240, F.241, F.294, N.304, E.305 Ligands: PHY.2, MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.171, A:G.176, A:S.177, A:S.178, A:Q.208, A:V.210, A:E.214, A:F.241, A:N.304, A:E.305 Water bridges: A:R.317, A:R.317 Salt bridges: A:K.133, A:K.133, A:K.171 pi-Stacking: A:F.169, A:F.169 ADP.15: 22 residues within 4Å: Chain B: K.133, F.169, K.171, S.175, G.176, S.177, S.178, V.181, E.207, Q.208, A.209, V.210, E.214, L.236, I.240, F.241, F.294, N.304, E.305 Ligands: PHY.16, MG.17, MG.18 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:K.171, B:G.176, B:S.177, B:S.178, B:E.207, B:Q.208, B:V.210, B:E.214, B:F.241, B:N.304 Water bridges: B:K.133, B:K.133, B:S.177, B:S.178, B:E.214, B:R.317 Salt bridges: B:K.133, B:K.133, B:K.171 pi-Stacking: B:F.169, B:F.169 ADP.26: 22 residues within 4Å: Chain C: K.133, F.169, K.171, S.175, G.176, S.177, S.178, V.181, E.207, Q.208, A.209, V.210, E.214, L.236, I.240, F.241, F.294, N.304, E.305 Ligands: PHY.27, MG.28, MG.29 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:K.171, C:G.176, C:S.177, C:S.178, C:E.207, C:Q.208, C:V.210, C:E.214, C:F.241, C:N.304, C:E.305 Water bridges: C:E.214, C:E.305, C:R.317, C:R.317 Salt bridges: C:K.133, C:K.133, C:K.171 pi-Stacking: C:F.169, C:F.169 ADP.40: 22 residues within 4Å: Chain D: K.133, F.169, K.171, S.175, G.176, S.177, S.178, V.181, E.207, Q.208, A.209, V.210, E.214, L.236, I.240, F.241, F.294, N.304, E.305 Ligands: PHY.41, MG.42, MG.43 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:K.171, D:G.176, D:S.177, D:S.178, D:Q.208, D:V.210, D:E.214, D:F.241, D:N.304 Water bridges: D:K.133, D:K.133, D:S.177, D:S.178, D:E.214, D:R.317 Salt bridges: D:K.133, D:K.133, D:K.171 pi-Stacking: D:F.169, D:F.169

4 x PHY: 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID(Non-covalent)

PHY.2: 17 residues within 4Å: Chain A: E.16, H.99, S.177, F.241, I.243, H.244, R.290, D.292, E.305, N.307, P.310, G.311, S.316, R.317 Ligands: ADP.1, MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.241, A:I.243 Hydrogen bonds: A:S.177, A:S.177, A:R.290, A:R.290, A:D.292, A:G.311, A:R.317 Water bridges: A:H.99, A:H.99, A:R.317, A:Y.318 Salt bridges: A:H.244, A:R.290, A:R.290 PHY.16: 17 residues within 4Å: Chain B: E.16, H.99, S.177, F.241, I.243, H.244, R.290, D.292, E.305, N.307, P.310, G.311, S.316, R.317 Ligands: ADP.15, MG.17, MG.18 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.241, B:I.243 Hydrogen bonds: B:S.177, B:R.290, B:R.290, B:D.292, B:G.311, B:R.317 Water bridges: B:E.16, B:D.292, B:N.307, B:N.307, B:N.307, B:R.317 Salt bridges: B:H.244, B:R.290, B:R.290 PHY.27: 17 residues within 4Å: Chain C: E.16, H.99, S.177, F.241, I.243, H.244, R.290, D.292, E.305, N.307, P.310, G.311, S.316, R.317 Ligands: ADP.26, MG.28, MG.29 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.241, C:I.243 Hydrogen bonds: C:S.177, C:S.177, C:R.290, C:R.290, C:G.311, C:R.317 Water bridges: C:N.307, C:N.307, C:R.317, C:Y.318 Salt bridges: C:H.244, C:R.290, C:R.290 PHY.41: 17 residues within 4Å: Chain D: E.16, H.99, S.177, F.241, I.243, H.244, R.290, D.292, E.305, N.307, P.310, G.311, S.316, R.317 Ligands: ADP.40, MG.42, MG.43 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.241, D:I.243 Hydrogen bonds: D:E.16, D:S.177, D:R.290, D:R.290, D:G.311, D:R.317 Water bridges: D:D.292, D:N.307, D:N.307, D:N.307, D:R.317 Salt bridges: D:H.244, D:R.290, D:R.290

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: G.176, E.305, N.307 Ligands: ADP.1, PHY.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.305, A:E.305, H2O.4 MG.4: 5 residues within 4Å: Chain A: D.292, E.305 Ligands: ADP.1, PHY.2, MG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.305, H2O.6, H2O.7 MG.17: 5 residues within 4Å: Chain B: G.176, E.305, N.307 Ligands: ADP.15, PHY.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.305, B:E.305, H2O.11 MG.18: 4 residues within 4Å: Chain B: D.292, E.305 Ligands: ADP.15, PHY.16 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.305, H2O.13, H2O.14 MG.28: 6 residues within 4Å: Chain C: G.176, E.305, N.307 Ligands: ADP.26, PHY.27, MG.29 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.305, C:E.305, H2O.18 MG.29: 5 residues within 4Å: Chain C: D.292, E.305 Ligands: ADP.26, PHY.27, MG.28 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.305, H2O.20, H2O.21 MG.42: 5 residues within 4Å: Chain D: G.176, E.305, N.307 Ligands: ADP.40, PHY.41 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.305, D:E.305, H2O.24 MG.43: 4 residues within 4Å: Chain D: D.292, E.305 Ligands: ADP.40, PHY.41 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.305, H2O.27, H2O.27

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

SO4.5: 3 residues within 4Å: Chain A: N.154, R.174, K.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.154 Water bridges: A:K.203, A:K.203 Salt bridges: A:R.174, A:K.203 SO4.6: 5 residues within 4Å: Chain A: D.105, R.174 Chain B: E.113, D.123, Q.125 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.125 Water bridges: B:I.124 Salt bridges: A:R.174 SO4.19: 3 residues within 4Å: Chain B: N.154, R.174, K.203 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.154 Water bridges: B:K.203, B:K.203 Salt bridges: B:R.174, B:K.203 SO4.30: 3 residues within 4Å: Chain C: N.154, R.174, K.203 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.154 Water bridges: C:K.203, C:K.203 Salt bridges: C:R.174, C:K.203 SO4.31: 5 residues within 4Å: Chain C: D.105, R.174 Chain D: E.113, D.123, Q.125 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.113, D:D.123, D:Q.125, C:D.105 Water bridges: D:I.124 Salt bridges: C:R.174 SO4.44: 3 residues within 4Å: Chain D: N.154, R.174, K.203 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.154 Water bridges: D:K.203, D:K.203 Salt bridges: D:R.174, D:K.203

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: S.66, K.81 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: K.183, N.185, Y.238, G.239 Ligand excluded by PLIP GOL.9: 1 residues within 4Å: Chain A: H.84 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: N.2, R.3 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: K.155, E.195, R.198 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: K.5, E.37, L.39, N.89 Ligand excluded by PLIP GOL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: R.158 Chain C: K.155 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: S.265, A.266, R.269 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: R.3, K.33, E.34 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: N.222, V.338, L.339, A.340, L.341 Chain C: V.160 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: E.37, L.39, M.51, K.82, N.89 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: E.26, N.30, F.312, T.313, S.314, P.319, L.329 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain B: K.50, C.64, Y.65, S.66 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain C: S.66, K.81 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: K.183, N.185, Y.238, G.239 Ligand excluded by PLIP GOL.34: 1 residues within 4Å: Chain C: H.84 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain C: N.2, R.3 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain C: K.155, E.195, R.198 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain C: K.5, E.37, L.39, N.89 Ligand excluded by PLIP GOL.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.39: 2 residues within 4Å: Chain A: K.155 Chain C: R.158 Ligand excluded by PLIP GOL.45: 3 residues within 4Å: Chain D: S.265, A.266, R.269 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain D: R.3, K.33, E.34 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain A: V.160 Chain D: N.222, V.338, L.339, A.340, L.341 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain D: E.37, L.39, M.51, K.82, N.89 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain D: E.26, N.30, F.312, T.313, S.314, P.319, L.329 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain D: K.50, C.64, Y.65, S.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roper, D.I. et al., The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). Proc. Natl. Acad. Sci. U.S.A. (2000)

Release Date

2001-06-28

Peptides

VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA: AC
VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA

VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA