SMTL ID : 6i5d.1

Crystal structure of an OXA-48 beta-lactamase synthetic mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: N.181, G.182, D.183, Y.184, I.185, E.207, L.208, D.209 Chain B: K.97 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.207, B:K.97 Water bridges: B:K.97, B:L.177 GOL.2: 7 residues within 4Å: Chain A: K.75, W.76, D.77, R.81, P.102, V.103, E.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.77, A:D.77, A:R.81 Water bridges: A:D.77 GOL.3: 6 residues within 4Å: Chain A: E.166, R.167, R.170 Chain B: E.166, R.167, R.170 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.170, A:R.170 Water bridges: A:E.166 GOL.19: 6 residues within 4Å: Chain B: N.13, F.16, Q.22, G.23, N.38, N.39 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.21, B:G.23, B:G.23, B:N.38, B:N.39 Water bridges: B:N.13, B:N.13 GOL.20: 5 residues within 4Å: Chain B: W.6, T.148, I.151, S.152, R.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.155, B:R.155 Water bridges: B:S.152 GOL.21: 7 residues within 4Å: Chain A: H.159, N.160, E.166, R.170 Chain B: K.68, D.69, R.167 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.68, B:K.68, B:D.69, B:R.167, B:R.167, A:H.159, A:N.160, A:R.170 GOL.22: 7 residues within 4Å: Chain A: D.209, D.210 Chain B: V.73, D.89, H.90, N.91, T.94 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.89, B:D.89, B:N.91, B:N.91, B:T.94 GOL.23: 5 residues within 4Å: Chain B: I.111, G.112, E.113, A.114, R.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.112, B:A.114, B:R.115 Water bridges: B:R.115 GOL.24: 8 residues within 4Å: Chain A: K.97, L.177, K.189 Chain B: N.181, G.182, D.183, Y.184, I.185 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.183, A:K.189 Water bridges: B:I.185, B:D.209, A:K.97, A:T.178, A:T.178 GOL.25: 8 residues within 4Å: Chain B: K.75, W.76, D.77, R.81, P.102, V.103, E.106 Ligands: GOL.27 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.77, B:R.81, B:E.106, B:E.106 Water bridges: B:W.86 GOL.26: 3 residues within 4Å: Chain B: A.46, N.127, R.144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.127 Water bridges: B:A.46, B:E.149, B:E.149, B:E.149 GOL.27: 6 residues within 4Å: Chain B: R.81, P.102, Q.105, E.106, R.109 Ligands: GOL.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.81, B:P.102, B:R.109, B:R.109 GOL.28: 5 residues within 4Å: Chain B: S.131, G.132, D.140, G.141, G.142 No protein-ligand interaction detected (PLIP)

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

CL.4: 2 residues within 4Å: Chain A: R.187 Chain B: R.187 Ligand excluded by PLIP

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 6 residues within 4Å: Chain A: A.50, K.54, V.101, Y.104, W.138, L.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.50 NO3.6: 5 residues within 4Å: Chain A: W.86, V.101, L.139, T.194, R.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.194, A:R.195, A:R.195 NO3.7: 5 residues within 4Å: Chain A: L.62, D.63, S.165, R.167, S.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.165, A:S.165, A:R.167 NO3.8: 4 residues within 4Å: Chain A: Q.22, K.41, R.42, Q.45 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.22, A:K.41, A:R.42, A:Q.45 Water bridges: A:R.42 NO3.9: 4 residues within 4Å: Chain A: R.155, K.156, H.159, K.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.155 Water bridges: A:R.155, A:R.155 NO3.29: 8 residues within 4Å: Chain B: A.50, S.51, K.54, S.99, V.101, Y.104, W.138, L.139 No protein-ligand interaction detected (PLIP)

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

EDO.10: 4 residues within 4Å: Chain A: E.5, W.28, S.152, R.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.155, A:R.155 EDO.11: 6 residues within 4Å: Chain A: N.13, F.16, Q.22, G.23, N.38, N.39 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.23, A:N.38, A:N.39 Water bridges: A:Q.22 EDO.12: 6 residues within 4Å: Chain A: A.46, G.126, N.127, R.144, I.145, E.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.144 EDO.13: 5 residues within 4Å: Chain A: F.47, L.48, E.197, K.198, I.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.197, A:K.198, A:I.199, A:I.199 EDO.14: 3 residues within 4Å: Chain A: L.64, V.66, R.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.64, A:Q.110, A:R.115, A:R.115 EDO.15: 6 residues within 4Å: Chain A: A.122, F.123, K.156, K.161, L.162, H.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.163 EDO.16: 9 residues within 4Å: Chain A: K.54, S.99, K.189, T.190, G.191, Y.192, W.202, L.227, Q.231 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.54, A:K.54, A:S.99, A:T.190, A:G.191, A:Y.192, A:W.202, A:Q.231 Water bridges: A:K.189 EDO.30: 4 residues within 4Å: Chain B: R.155, K.156, H.159, K.161 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.155 EDO.31: 4 residues within 4Å: Chain B: L.208, D.209, D.210, N.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.209, B:D.210, B:D.210 Water bridges: B:W.213 EDO.32: 9 residues within 4Å: Chain B: T.178, A.188, K.189, T.190, G.191, Y.192, W.202, L.227, Q.231 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.178, B:T.178, B:K.189, B:T.190, B:G.191, B:Y.192, B:Q.231 Water bridges: B:K.189

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

PEG.17: 6 residues within 4Å: Chain A: V.73, D.89, H.90, N.91, T.94 Chain B: D.209 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.91, A:T.94, B:D.209 Water bridges: B:D.210

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

PO4.18: 3 residues within 4Å: Chain B: E.113, S.117, I.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.117 Water bridges: B:E.113, B:S.117, B:I.130, B:I.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dabos, L. et al., Substrate specificity of an OXA-48 beta-lactamase synthetic mutant. To be published

Release Date

2020-03-04

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase