SMTL ID : 1jgt.1

CRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.253, D.351, K.443 Ligands: APC.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.253, A:D.351, H2O.1 MG.4: 5 residues within 4Å: Chain B: D.253, D.351, K.423 Ligands: APC.5, CMA.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.253, B:D.351, H2O.15

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 20 residues within 4Å: Chain A: V.247, L.248, S.249, G.251, I.252, D.253, S.254, V.271, S.272, M.273, L.330, L.333, T.346, G.347, Y.348, D.351, K.423, K.443 Ligands: MG.1, CMA.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.249, A:I.252, A:D.253, A:S.254, A:M.273, A:M.273, A:G.347, A:G.347 Water bridges: A:G.251, A:G.251, A:G.349, A:D.351 Salt bridges: A:K.423, A:K.443 APC.5: 21 residues within 4Å: Chain B: V.247, L.248, S.249, G.251, I.252, D.253, S.254, V.271, S.272, M.273, L.330, L.333, T.346, G.347, Y.348, D.351, K.423, K.443, L.444 Ligands: MG.4, CMA.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.249, B:G.251, B:I.252, B:D.253, B:S.254, B:M.273, B:M.273, B:G.347, B:G.347, B:G.347, B:L.444 Water bridges: B:S.249, B:G.349 Salt bridges: B:K.423, B:K.443

2 x CMA: N2-(CARBOXYETHYL)-L-ARGININE(Non-covalent)

CMA.3: 9 residues within 4Å: Chain A: Y.326, Y.348, G.349, D.351, I.352, D.373, L.380, E.382 Ligands: APC.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.326, A:Y.326, A:Y.348 Hydrogen bonds: A:G.349, A:D.351, A:D.351, A:I.352 Water bridges: A:A.350 Salt bridges: A:D.373, A:E.382 CMA.6: 13 residues within 4Å: Chain B: Y.326, Y.348, G.349, A.350, D.351, I.352, M.357, D.373, L.380, E.382, K.443 Ligands: MG.4, APC.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.326, B:Y.348 Hydrogen bonds: B:Y.326, B:G.349, B:D.351, B:I.352 Water bridges: B:A.350, B:A.350, B:D.373, B:D.373, B:T.376, B:T.376 Salt bridges: B:D.373, B:E.382, B:K.443

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain B: L.245, D.269, T.270, R.294, H.295, D.338, R.342 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.294, B:R.342 Water bridges: B:D.338 GOL.8: 8 residues within 4Å: Chain B: L.13, A.14, S.15, P.24, D.36, A.47, A.48, T.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.36 Water bridges: B:I.37 GOL.9: 1 residues within 4Å: Chain B: H.372 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: R.402, D.406 Chain B: S.213, R.215 Ligands: GOL.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:S.213, B:S.213 Hydrogen bonds: A:R.402 GOL.11: 5 residues within 4Å: Chain B: R.215, L.217, L.407, S.410 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.215, B:R.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, M.T. et al., Structure of beta-lactam synthetase reveals how to synthesize antibiotics instead of asparagine. Nat.Struct.Biol. (2001)

Release Date

2001-12-28

Peptides

BETA-LACTAM SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BETA-LACTAM SYNTHETASE

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