SMTL ID : 7q3t.1 (1 other biounit)

Crystal structure of the OmpK36 D insertion chimera from Klebsiella pneumonia

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-trimer

Ligands

28 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.1: 11 residues within 4Å: Chain A: Q.264, Y.265, P.273, S.274, V.275, V.300, G.301, V.314, Y.316, V.338 Ligands: C8E.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.273, A:V.275, A:V.275 Hydrogen bonds: A:S.274 C8E.2: 8 residues within 4Å: Chain A: G.20, H.22, F.24, L.340, G.341, L.342 Chain C: Y.92, Y.152 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.24, A:L.342, C:Y.92, C:Y.92, C:Y.92 C8E.5: 11 residues within 4Å: Chain A: E.219, Y.221, T.222, G.223, Y.238, Q.240, Y.242, N.254, K.255, D.284 Ligands: C8E.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.242, A:Y.242, A:N.254, A:K.255, A:D.284 Hydrogen bonds: A:Y.242 C8E.6: 2 residues within 4Å: Chain A: F.195 Ligands: C8E.5 No protein-ligand interaction detected (PLIP) C8E.7: 2 residues within 4Å: Chain A: Y.238 Ligands: C8E.11 No protein-ligand interaction detected (PLIP) C8E.8: 8 residues within 4Å: Chain A: Y.92, Y.152 Chain B: G.20, H.22, F.24, L.340, G.341, L.342 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.24, B:L.342, A:Y.92, A:Y.92 C8E.9: 4 residues within 4Å: Chain A: Y.265, F.267, P.273 Ligands: C8E.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.265, A:Y.265, A:F.267, A:P.273 C8E.10: 4 residues within 4Å: Chain A: I.187, W.188, I.191 Ligands: C8E.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.187 C8E.11: 4 residues within 4Å: Chain A: Y.238, F.259 Ligands: C8E.7, C8E.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.238, A:F.259, A:F.259 C8E.12: 2 residues within 4Å: Chain A: V.275, Y.277 No protein-ligand interaction detected (PLIP) C8E.13: 1 residues within 4Å: Ligands: C8E.15 No protein-ligand interaction detected (PLIP) C8E.14: 3 residues within 4Å: Chain A: I.191, Y.227 Ligands: C8E.10 No protein-ligand interaction detected (PLIP) C8E.15: 9 residues within 4Å: Chain A: G.194, G.223, G.224, L.225, S.236, Y.238, V.261 Ligands: C8E.11, C8E.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.225 Hydrogen bonds: A:S.236 C8E.16: 14 residues within 4Å: Chain B: I.191, A.193, F.195, G.223, G.224, L.225, K.226, Y.227, A.235, S.236, Q.237, Y.238, F.259 Ligands: C8E.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.191, B:L.225, B:Y.227 Hydrogen bonds: B:S.236 C8E.17: 5 residues within 4Å: Chain B: F.259, V.261, Y.277 Ligands: C8E.16, C8E.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.259, B:V.261, B:Y.277 C8E.18: 7 residues within 4Å: Chain B: V.261, A.263, V.275, A.276, Y.277, V.298 Ligands: C8E.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.263, B:V.275, B:V.275, B:Y.277 C8E.19: 4 residues within 4Å: Chain B: Y.227, N.230, I.232 Ligands: C8E.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.232 C8E.20: 7 residues within 4Å: Chain B: F.24, V.300, G.301, V.314, Y.316, V.338 Ligands: C8E.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.300, B:V.314 C8E.23: 3 residues within 4Å: Chain B: F.139, L.142, V.143 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.139, B:F.139, B:L.142, B:V.143 C8E.24: 3 residues within 4Å: Chain B: I.232, Y.265 Ligands: C8E.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.265 C8E.25: 5 residues within 4Å: Chain B: V.275, V.298, V.300, I.318, L.320 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.275, B:V.298, B:V.300, B:I.318 C8E.26: 8 residues within 4Å: Chain B: A.263, Q.264, P.273, S.274, V.275, V.300, G.301 Ligands: C8E.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.273, B:V.300 C8E.27: 4 residues within 4Å: Chain B: Y.221, Y.238, Q.240, Y.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.240, B:Y.242 C8E.30: 7 residues within 4Å: Chain C: I.232, A.263, Q.264, Y.265, P.273, S.274, V.275 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.232, C:Y.265, C:P.273, C:V.275 C8E.31: 1 residues within 4Å: Chain C: A.302 No protein-ligand interaction detected (PLIP) C8E.32: 5 residues within 4Å: Chain C: V.275, A.276, Y.277, K.296, V.298 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.275, C:V.298 Hydrogen bonds: C:K.296 C8E.33: 7 residues within 4Å: Chain C: A.132, L.150, Y.152, D.177, F.179, H.199, K.201 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.152, C:Y.152 C8E.34: 13 residues within 4Å: Chain C: F.148, L.150, T.181, S.182, L.183, F.195, A.196, Y.197, Y.221, T.222, G.223, Y.238, Q.240 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.148, C:L.150, C:T.181, C:L.183 Hydrogen bonds: C:T.222

6 x LI: LITHIUM ION(Non-covalent)

LI.3: 3 residues within 4Å: Chain A: N.319, L.321, T.334 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.321, A:T.334, H2O.5, H2O.7, H2O.7 LI.4: 3 residues within 4Å: Chain A: R.214, N.243, N.254 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:R.214, H2O.2, H2O.6, H2O.7 LI.21: 3 residues within 4Å: Chain B: N.319, L.321, T.334 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:L.321, B:T.334, H2O.9, H2O.10, H2O.12 LI.22: 3 residues within 4Å: Chain B: R.214, N.243, N.254 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:R.214, H2O.10, H2O.12, H2O.13 LI.28: 3 residues within 4Å: Chain C: N.319, L.321, T.334 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.319, C:L.321, C:T.334, H2O.17, H2O.18 LI.29: 3 residues within 4Å: Chain C: R.214, N.243, N.254 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:R.214, H2O.16, H2O.18, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

David, S. et al., Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae. Plos Pathog. (2022)

Release Date

2022-07-06

Peptides

OmpK36: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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OmpK36

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