SMTL ID : 5fvn.1 (1 other biounit)

X-ray crystal structure of Enterobacter cloacae OmpE36 porin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

1 x GP1- Z9M- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO.1: 8 residues within 4Å: Chain A: D.174, K.198, R.213 Ligands: KDO.16, FTT.17, FTT.18, FTT.19, FTT.30 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.174, A:D.174 Water bridges: A:K.152, B:D.25, B:D.25, A:K.198, A:R.213 Salt bridges: A:K.198, A:K.198, A:R.213

2 x GP1- Z9M- KDO- KDO- GMH: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO-KDO-GMH.2: 13 residues within 4Å: Chain B: K.152, E.159, D.160, D.174, K.198, R.199, T.200, S.201, R.213 Ligands: FTT.31, FTT.32, FTT.33, FTT.48 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Water bridges: C:S.24, C:S.24, C:D.25, C:D.25, C:D.25, C:D.30, C:D.30, B:S.201, B:K.198, B:K.198 Hydrogen bonds: B:D.174, B:K.152, B:E.159, B:E.159, B:D.160, B:D.160, B:S.201, B:D.174 Salt bridges: B:K.152, B:K.198, B:R.213 GP1-Z9M-KDO-KDO-GMH.3: 14 residues within 4Å: Chain C: N.210, G.211, R.213, E.215, Y.238, N.239, N.250 Ligands: CA.47, FTT.50, FTT.51, FTT.52, FTT.53, MYR.54, DAO.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.239, C:N.239, C:E.215, C:Y.238 Water bridges: C:N.210, C:N.210, C:D.212, C:D.212, C:D.212, C:N.239, C:N.250

1 x GP1- Z9M- KDO- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO-KDO.4: 13 residues within 4Å: Chain C: K.152, E.159, D.160, D.174, K.198, R.199, T.200, S.201, R.213 Ligands: FTT.22, FTT.57, FTT.58, FTT.59 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.174, C:K.152, C:E.159, C:D.160, C:D.160, C:S.201, C:D.174, C:K.198 Water bridges: A:D.25, A:D.25, C:R.199, C:S.201, C:D.212, C:R.213 Salt bridges: C:K.152, C:K.198, C:R.213

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

SO4.5: 4 residues within 4Å: Chain A: N.69 Chain B: N.69 Chain C: N.69 Ligands: C8E.40 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:N.69, B:N.69, B:N.69, A:N.69 Water bridges: C:N.69, C:S.71

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

C8E.6: 4 residues within 4Å: Chain A: N.204, N.210, G.211, D.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 C8E.7: 1 residues within 4Å: Chain A: Y.182 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.182, A:Y.182 C8E.8: 3 residues within 4Å: Chain A: L.184, G.185, F.188 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.188 C8E.9: 3 residues within 4Å: Chain A: F.188, Y.223 Ligands: C8E.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.188, A:Y.223 C8E.10: 2 residues within 4Å: Chain A: V.257, Y.273 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.257, A:Y.273, A:Y.273 C8E.11: 7 residues within 4Å: Chain A: Q.29, F.110, G.111, D.113, Y.293, K.313, I.333 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.110, A:I.333 C8E.12: 7 residues within 4Å: Chain A: L.20, Y.22, Y.35, Q.59, Q.61, W.72, E.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:Y.22, A:Q.59, A:Q.61, A:Q.61 C8E.13: 3 residues within 4Å: Chain A: V.257, V.271, V.294 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.257, A:V.271, A:V.294 C8E.14: 2 residues within 4Å: Chain A: F.188 Ligands: C8E.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.188, A:F.188 C8E.24: 3 residues within 4Å: Chain B: Y.217, Q.236, Y.238 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.217, B:Q.236 C8E.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) C8E.26: 5 residues within 4Å: Chain B: L.20, Y.22, Y.35, Q.59, E.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.59 Water bridges: B:Y.22, B:Y.35, B:Q.61, B:Q.61 C8E.27: 3 residues within 4Å: Chain B: Y.261, F.263 Ligands: C8E.28 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.261, B:F.263, B:F.263 C8E.28: 2 residues within 4Å: Chain B: I.228 Ligands: C8E.27 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.228, B:I.228 C8E.36: 2 residues within 4Å: Chain C: A.298, T.308 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.308 C8E.37: 3 residues within 4Å: Chain C: F.145, I.180 Ligands: FTT.50 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.145, C:I.180 C8E.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) C8E.39: 6 residues within 4Å: Chain C: G.219, G.220, A.232, Y.234, F.255 Ligands: C8E.43 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.232, C:Y.234 C8E.40: 3 residues within 4Å: Chain C: E.68, N.69 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.68, C:N.69 C8E.41: 4 residues within 4Å: Chain C: I.180, Y.182, I.190 Ligands: C8E.42 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.180, C:Y.182, C:Y.182, C:Y.182, C:I.190 C8E.42: 4 residues within 4Å: Chain C: V.140, L.143 Ligands: C8E.41, FTT.52 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.140, C:L.143 C8E.43: 7 residues within 4Å: Chain C: I.190, G.191, G.219, G.220, Y.234 Ligands: C8E.39, DAO.55 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.190, C:Y.234, C:Y.234 C8E.44: 6 residues within 4Å: Chain C: V.296, G.297, A.298, V.310, Y.312, V.334 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.310, C:Y.312, C:Y.312, C:V.334 C8E.45: 4 residues within 4Å: Chain C: A.259, Q.260, P.269, V.271 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.269, C:V.271, C:V.271

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

PO4.15: 4 residues within 4Å: Chain A: G.116, S.117, R.170, R.242 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.117, A:S.117, A:R.242 Water bridges: A:S.117, A:S.117 Salt bridges: A:R.170 PO4.29: 4 residues within 4Å: Chain B: G.116, S.117, R.170, R.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.117, B:S.117, B:R.242 Water bridges: B:S.117 Salt bridges: B:R.170 PO4.46: 4 residues within 4Å: Chain C: G.116, S.117, R.170, R.242 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.117 Water bridges: C:R.242 Salt bridges: C:R.170

1 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)

KDO.16: 9 residues within 4Å: Chain A: K.152, E.159, D.160, K.198, R.199, T.200, S.201 Ligands: GP1-Z9M-KDO.1, GP1-Z9M-KDO.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.152, A:E.159, A:D.160, A:D.160, A:S.201 Water bridges: A:S.201 Salt bridges: A:K.152

16 x FTT: 3-HYDROXY-TETRADECANOIC ACID(Non-covalent)(Non-functional Binders)

FTT.17: 9 residues within 4Å: Chain A: Y.90, Y.149, G.151 Chain B: G.19, H.21, F.23, G.337, L.338 Ligands: GP1-Z9M-KDO.1 Ligand excluded by PLIP FTT.18: 7 residues within 4Å: Chain A: F.88, Y.149, D.174 Ligands: GP1-Z9M-KDO.1, GP1-Z9M-KDO.1, FTT.19, DAO.21 Ligand excluded by PLIP FTT.19: 11 residues within 4Å: Chain A: F.88, A.129, Y.131, V.147, Y.149, D.174, V.176, R.213 Ligands: GP1-Z9M-KDO.1, FTT.18, MYR.20 Ligand excluded by PLIP FTT.22: 5 residues within 4Å: Chain A: F.23, V.334, L.336 Ligands: GP1-Z9M-KDO-KDO.4, DAO.23 Ligand excluded by PLIP FTT.30: 2 residues within 4Å: Chain B: F.23 Ligands: GP1-Z9M-KDO.1 Ligand excluded by PLIP FTT.31: 11 residues within 4Å: Chain B: Y.90, Y.149, G.151 Chain C: G.19, H.21, F.23, G.337, L.338 Ligands: GP1-Z9M-KDO-KDO-GMH.2, FTT.32, DAO.49 Ligand excluded by PLIP FTT.32: 7 residues within 4Å: Chain B: Y.149, D.174 Ligands: GP1-Z9M-KDO-KDO-GMH.2, GP1-Z9M-KDO-KDO-GMH.2, FTT.31, FTT.33, DAO.35 Ligand excluded by PLIP FTT.33: 11 residues within 4Å: Chain B: F.88, A.129, Y.131, V.147, Y.149, D.174, V.176, R.213 Ligands: GP1-Z9M-KDO-KDO-GMH.2, FTT.32, MYR.34 Ligand excluded by PLIP FTT.48: 3 residues within 4Å: Chain C: F.23 Ligands: GP1-Z9M-KDO-KDO-GMH.2, DAO.49 Ligand excluded by PLIP FTT.50: 12 residues within 4Å: Chain C: F.145, A.146, G.178, S.179, I.180, S.196, R.213 Ligands: GP1-Z9M-KDO-KDO-GMH.3, C8E.37, FTT.53, DAO.56, MYR.60 Ligand excluded by PLIP FTT.51: 7 residues within 4Å: Chain C: E.215, Y.217 Ligands: GP1-Z9M-KDO-KDO-GMH.3, GP1-Z9M-KDO-KDO-GMH.3, FTT.52, MYR.54, DAO.56 Ligand excluded by PLIP FTT.52: 8 residues within 4Å: Chain C: E.215, Y.217, Y.238 Ligands: GP1-Z9M-KDO-KDO-GMH.3, C8E.42, FTT.51, MYR.54, DAO.55 Ligand excluded by PLIP FTT.53: 4 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO-GMH.3, FTT.50, DAO.56, MYR.60 Ligand excluded by PLIP FTT.57: 11 residues within 4Å: Chain A: G.19, H.21, F.23, L.336, G.337, L.338 Chain C: Y.90, Y.149, G.151 Ligands: GP1-Z9M-KDO-KDO.4, FTT.58 Ligand excluded by PLIP FTT.58: 8 residues within 4Å: Chain C: Y.149, D.174 Ligands: GP1-Z9M-KDO-KDO.4, GP1-Z9M-KDO-KDO.4, DAO.23, FTT.57, FTT.59, DAO.61 Ligand excluded by PLIP FTT.59: 13 residues within 4Å: Chain C: F.88, A.129, T.130, Y.131, V.147, Y.149, D.174, V.176, R.213 Ligands: GP1-Z9M-KDO-KDO.4, FTT.58, MYR.60, DAO.61 Ligand excluded by PLIP

4 x MYR: MYRISTIC ACID(Non-covalent)(Non-functional Binders)

MYR.20: 2 residues within 4Å: Chain A: R.213 Ligands: FTT.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.213 MYR.34: 2 residues within 4Å: Chain B: R.213 Ligands: FTT.33 No protein-ligand interaction detected (PLIP) MYR.54: 3 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO-GMH.3, FTT.51, FTT.52 No protein-ligand interaction detected (PLIP) MYR.60: 6 residues within 4Å: Chain C: V.147, V.176, R.213 Ligands: FTT.50, FTT.53, FTT.59 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.147, C:V.176 Water bridges: C:R.213

7 x DAO: LAURIC ACID(Non-functional Binders)(Non-covalent)

DAO.21: 1 residues within 4Å: Ligands: FTT.18 No protein-ligand interaction detected (PLIP) DAO.23: 3 residues within 4Å: Chain A: L.336 Ligands: FTT.22, FTT.58 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.336 DAO.35: 1 residues within 4Å: Ligands: FTT.32 No protein-ligand interaction detected (PLIP) DAO.49: 2 residues within 4Å: Ligands: FTT.31, FTT.48 No protein-ligand interaction detected (PLIP) DAO.55: 9 residues within 4Å: Chain C: T.192, Y.217, T.218, G.219, Y.234, Q.236, Y.238 Ligands: C8E.43, FTT.52 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.234 DAO.56: 4 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO-GMH.3, FTT.50, FTT.51, FTT.53 No protein-ligand interaction detected (PLIP) DAO.61: 2 residues within 4Å: Ligands: FTT.58, FTT.59 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.47: 4 residues within 4Å: Chain C: N.210, N.239, N.250 Ligands: GP1-Z9M-KDO-KDO-GMH.3 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.210, H2O.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arunmanee, W. et al., Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-08-10

Peptides

OMPC PORIN: 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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OMPC PORIN

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