SMTL ID : 5gwa.1

Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with avibactam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x NXL: (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide(Covalent)

NXL.1: 19 residues within 4Å: Chain A: Q.46, S.47, K.50, W.84, S.111, N.113, E.147, H.151, T.197, R.201, K.215, T.216, G.217, S.218 Chain B: P.81, N.82 Ligands: SO4.3, CL.7, GOL.25 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.84 Hydrogen bonds: A:S.47, A:S.111, A:N.113, A:T.197, A:T.216, A:S.218, B:N.82 Water bridges: A:Q.46, A:W.84 Salt bridges: A:R.201, A:K.215 NXL.26: 19 residues within 4Å: Chain A: P.81, N.82 Chain B: Q.46, S.47, K.50, W.84, S.111, N.113, E.147, H.151, T.197, R.201, K.215, T.216, G.217, S.218 Ligands: SO4.28, CL.32, GOL.50 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:N.82, B:S.47, B:S.111, B:N.113, B:T.216, B:S.218 Hydrophobic interactions: B:W.84 Water bridges: B:Q.46, B:W.84 Salt bridges: B:R.201, B:K.215

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

SO4.2: 4 residues within 4Å: Chain A: Y.175, V.211, T.237, H.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.175, A:Y.175, A:T.237 Salt bridges: A:H.243 SO4.3: 11 residues within 4Å: Chain A: T.197, G.198, P.199, R.201, E.261 Chain B: K.76, P.81, K.88, P.92 Ligands: NXL.1, NA.12 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.198, B:P.92 Water bridges: A:R.201, B:K.76 Salt bridges: A:R.201, B:K.76, B:K.88 SO4.4: 1 residues within 4Å: Chain A: K.182 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.182 SO4.5: 4 residues within 4Å: Chain A: N.127, K.128, N.131 Ligands: NA.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.131 Water bridges: A:N.127, A:K.128, A:K.128, A:K.128 Salt bridges: A:K.128 SO4.27: 4 residues within 4Å: Chain B: Y.175, V.211, T.237, H.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.175, B:Y.175 Salt bridges: B:H.243 SO4.28: 11 residues within 4Å: Chain A: K.76, P.81, K.88, P.92 Chain B: T.197, G.198, P.199, R.201, E.261 Ligands: NXL.26, NA.37 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.198, A:P.92 Water bridges: B:R.201, A:K.76 Salt bridges: B:R.201, A:K.76, A:K.88 SO4.29: 1 residues within 4Å: Chain B: K.182 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.182 SO4.30: 4 residues within 4Å: Chain B: N.127, K.128, N.131 Ligands: NA.40 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.131 Water bridges: B:N.127, B:K.128, B:K.128, B:K.128 Salt bridges: B:K.128

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

CL.6: 6 residues within 4Å: Chain A: F.174, N.177, E.178, I.179, L.180, Y.185 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: T.83, W.84, N.113, H.151 Ligands: NXL.1 Ligand excluded by PLIP CL.31: 6 residues within 4Å: Chain B: F.174, N.177, E.178, I.179, L.180, Y.185 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain B: T.83, W.84, N.113, H.151 Ligands: NXL.26 Ligand excluded by PLIP

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

NA.8: 4 residues within 4Å: Chain A: L.98, S.99, E.102 Ligands: NA.14 Ligand excluded by PLIP NA.9: 3 residues within 4Å: Chain A: K.105, S.106, H.110 Ligand excluded by PLIP NA.10: 5 residues within 4Å: Chain A: E.39, K.40, T.163, D.165 Ligands: NA.11 Ligand excluded by PLIP NA.11: 5 residues within 4Å: Chain A: N.140, T.163, D.165, A.166 Ligands: NA.10 Ligand excluded by PLIP NA.12: 6 residues within 4Å: Chain A: G.198, P.199, K.200, E.261 Chain B: K.76 Ligands: SO4.3 Ligand excluded by PLIP NA.13: 7 residues within 4Å: Chain A: T.195, T.196, T.197, P.199, K.203, H.214 Ligands: NA.19 Ligand excluded by PLIP NA.14: 3 residues within 4Å: Chain A: K.71, E.97 Ligands: NA.8 Ligand excluded by PLIP NA.15: 5 residues within 4Å: Chain A: G.124, G.125, N.127, K.128 Ligands: SO4.5 Ligand excluded by PLIP NA.16: 5 residues within 4Å: Chain A: M.150, A.153, W.154, V.156, Q.157 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain A: G.28, I.29, E.30, D.31, H.243 Ligand excluded by PLIP NA.18: 6 residues within 4Å: Chain A: L.79, K.88, Y.91, P.92, N.93, G.94 Ligand excluded by PLIP NA.19: 7 residues within 4Å: Chain A: M.192, I.193, T.195, K.203, V.212, H.214 Ligands: NA.13 Ligand excluded by PLIP NA.20: 5 residues within 4Å: Chain A: L.15, A.20, K.21, V.22, N.38 Ligand excluded by PLIP NA.21: 5 residues within 4Å: Chain A: S.134, V.138, K.139, N.140, I.141 Ligand excluded by PLIP NA.22: 6 residues within 4Å: Chain A: T.221, G.225, T.227, S.253, S.254, E.255 Ligand excluded by PLIP NA.23: 6 residues within 4Å: Chain A: S.218, S.219, T.227, A.229, T.230 Chain B: N.82 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain A: T.126, N.127, I.143, K.144 Ligand excluded by PLIP NA.33: 4 residues within 4Å: Chain B: L.98, S.99, E.102 Ligands: NA.39 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Chain B: K.105, S.106, H.110 Ligand excluded by PLIP NA.35: 5 residues within 4Å: Chain B: E.39, K.40, T.163, D.165 Ligands: NA.36 Ligand excluded by PLIP NA.36: 5 residues within 4Å: Chain B: N.140, T.163, D.165, A.166 Ligands: NA.35 Ligand excluded by PLIP NA.37: 6 residues within 4Å: Chain A: K.76 Chain B: G.198, P.199, K.200, E.261 Ligands: SO4.28 Ligand excluded by PLIP NA.38: 7 residues within 4Å: Chain B: T.195, T.196, T.197, P.199, K.203, H.214 Ligands: NA.44 Ligand excluded by PLIP NA.39: 3 residues within 4Å: Chain B: K.71, E.97 Ligands: NA.33 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain B: G.124, G.125, N.127, K.128 Ligands: SO4.30 Ligand excluded by PLIP NA.41: 5 residues within 4Å: Chain B: M.150, A.153, W.154, V.156, Q.157 Ligand excluded by PLIP NA.42: 5 residues within 4Å: Chain B: G.28, I.29, E.30, D.31, H.243 Ligand excluded by PLIP NA.43: 6 residues within 4Å: Chain B: L.79, K.88, Y.91, P.92, N.93, G.94 Ligand excluded by PLIP NA.44: 7 residues within 4Å: Chain B: M.192, I.193, T.195, K.203, V.212, H.214 Ligands: NA.38 Ligand excluded by PLIP NA.45: 5 residues within 4Å: Chain B: L.15, A.20, K.21, V.22, N.38 Ligand excluded by PLIP NA.46: 5 residues within 4Å: Chain B: S.134, V.138, K.139, N.140, I.141 Ligand excluded by PLIP NA.47: 6 residues within 4Å: Chain B: T.221, G.225, T.227, S.253, S.254, E.255 Ligand excluded by PLIP NA.48: 6 residues within 4Å: Chain A: N.82 Chain B: S.218, S.219, T.227, A.229, T.230 Ligand excluded by PLIP NA.49: 4 residues within 4Å: Chain B: T.126, N.127, I.143, K.144 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 9 residues within 4Å: Chain A: Q.46, M.150, H.151, W.154, Q.157, S.219, D.220 Chain B: N.82 Ligands: NXL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.46, A:H.151, A:Q.157, A:D.220 Water bridges: A:A.153 GOL.50: 9 residues within 4Å: Chain A: N.82 Chain B: Q.46, M.150, H.151, W.154, Q.157, S.219, D.220 Ligands: NXL.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.46, B:Q.157, B:D.220 Water bridges: B:H.151, B:A.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, W. et al., Structural Insights into the TLA-3 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam and OP0595. Antimicrob. Agents Chemother. (2017)

Release Date

2017-07-12

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-lactamase

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