SMTL ID : 5hap.1

OXA-48 beta-lactamase - S70A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.182 Chain B: R.182 Ligand excluded by PLIP

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 3 residues within 4Å: Chain A: A.41, F.42, P.193 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.139, A:R.139

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 2 residues within 4Å: Chain A: Q.74, R.76 No protein-ligand interaction detected (PLIP) PGE.4: 4 residues within 4Å: Chain A: R.150, K.151, H.154, K.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.156 Water bridges: A:R.150

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: N.39, Q.40, A.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.39, A:A.41 NA.11: 3 residues within 4Å: Chain B: N.155, E.161, Q.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.164 Water bridges: B:N.155, B:L.157

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 1 residues within 4Å: Chain A: R.104 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.104, A:D.130 PEG.7: 4 residues within 4Å: Chain A: D.58, S.160, R.162, S.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.160, A:R.162 Water bridges: A:R.162 PEG.8: 4 residues within 4Å: Chain A: I.78, T.80, Y.93 Ligands: PEG.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.80 Water bridges: A:T.80, A:T.80 PEG.9: 7 residues within 4Å: Chain A: I.180, L.204, D.205 Chain B: N.86, I.88, T.89, K.92 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.86, B:K.92, A:D.205 Water bridges: B:H.66, A:N.207 PEG.12: 3 residues within 4Å: Chain B: R.150, K.151, H.154 No protein-ligand interaction detected (PLIP) PEG.13: 5 residues within 4Å: Chain A: K.92, Y.93 Chain B: G.177, D.178 Ligands: PEG.8 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.92 Water bridges: B:G.177, B:D.178 PEG.14: 5 residues within 4Å: Chain B: W.1, W.23, T.143, I.146, R.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.143, B:R.150 PEG.15: 3 residues within 4Å: Chain A: G.177 Chain B: K.92, Y.93 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.177

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 4 residues within 4Å: Chain A: W.23, I.146, S.147, R.150 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.23, A:W.23, A:I.146 Hydrogen bonds: A:S.147, A:R.150 Water bridges: A:R.150

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 4 residues within 4Å: Chain B: L.57, D.58, L.59, G.60 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.162, B:R.162, B:R.162

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

EDO.17: 2 residues within 4Å: Chain A: R.162 Chain B: E.161 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain A: D.205 Chain B: D.84, H.85, N.86, T.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.86, B:T.89 EDO.19: 4 residues within 4Å: Chain A: H.66 Chain B: E.25, N.26, H.154 No protein-ligand interaction detected (PLIP) EDO.20: 1 residues within 4Å: Chain B: T.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.76 Water bridges: B:D.77, B:D.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stojanoski, V. et al., Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain. Biochemistry (2016)

Release Date

2016-09-07

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase