SMTL ID : 5fvn.2 (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

3 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: 6 residues within 4Å: Chain A: K.277, K.292 Ligands: FTT.19, FTT.20, FTT.21, FTT.22 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.277, A:K.277, A:K.292 GP1-Z9M-KDO.2: 8 residues within 4Å: Chain A: D.174, K.198, R.213 Ligands: KDO.18, FTT.25, FTT.26, FTT.27, FTT.34 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Water bridges: B:S.24, B:S.24, B:D.25, B:D.30, A:R.213, A:R.213 Hydrogen bonds: A:D.174, A:D.174, A:D.174, A:K.198 Salt bridges: A:K.198, A:K.198, A:R.213 GP1-Z9M-KDO.3: 8 residues within 4Å: Chain B: D.174, K.198, R.213 Ligands: KDO.33, FTT.36, FTT.37, FTT.38, FTT.46 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain B Water bridges: C:S.24, C:S.24, C:D.25, C:D.30, B:Y.149, B:Y.149, B:R.213, B:R.213, B:R.213 Hydrogen bonds: B:D.174, B:D.174, B:D.174, B:D.174, B:K.198 Salt bridges: B:K.198, B:K.198, B:R.213

1 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.4: 14 residues within 4Å: Chain C: N.210, G.211, E.215, Y.238, N.239, N.250, K.251 Ligands: CA.45, FTT.47, FTT.48, FTT.49, FTT.50, DAO.52, DAO.53 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.215, C:N.239, C:Q.236 Water bridges: C:E.215, C:N.210, C:N.210, C:D.212, C:D.212, C:D.212, C:N.250, C:E.215, C:E.215 Salt bridges: C:K.251

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.5: 14 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.30, FTT.54, FTT.55, FTT.56, DAO.58 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:D.174, C:D.174, C:K.152, C:E.159, C:E.159, C:D.160, C:S.201, C:D.174, C:D.174, C:K.198 Water bridges: C:K.152, A:S.24, A:S.24, A:S.24, A:D.25, A:D.30, A:D.30, A:D.30, 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)

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

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

C8E.7: 3 residues within 4Å: Chain A: A.298, Y.309, V.310 No protein-ligand interaction detected (PLIP) C8E.8: 3 residues within 4Å: Chain A: Y.273 Ligands: C8E.10, FTT.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.273 C8E.9: 3 residues within 4Å: Chain A: V.296, V.310, Y.312 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.296, A:V.310 C8E.10: 5 residues within 4Å: Chain A: V.271, A.272, Y.273, V.294 Ligands: C8E.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.271, A:V.294 C8E.11: 3 residues within 4Å: Chain A: F.145, V.147, G.178 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.145, A:V.147 C8E.12: 5 residues within 4Å: Chain A: T.192, Y.217, T.218, G.219, Q.236 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.217 C8E.13: 3 residues within 4Å: Chain A: L.139, V.140, D.141 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.141 C8E.14: 2 residues within 4Å: Chain A: N.70, W.72 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.70 C8E.15: 1 residues within 4Å: Chain A: I.190 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.190 C8E.31: 4 residues within 4Å: Chain B: Y.217, Y.234, Q.236, Y.238 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.234 C8E.41: 5 residues within 4Å: Chain C: G.178, S.179, T.192, V.194 Ligands: FTT.47 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.192, C:V.194 C8E.42: 1 residues within 4Å: Chain C: V.294 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.294 C8E.43: 4 residues within 4Å: Chain C: L.336 Ligands: FTT.36, DAO.40, FTT.46 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.336

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

PO4.16: 4 residues within 4Å: Chain A: G.116, S.117, R.170, R.242 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.117, A:S.117, A:R.242 Water bridges: A:S.117, B:E.66 Salt bridges: A:R.170 PO4.32: 4 residues within 4Å: Chain B: G.116, S.117, R.170, R.242 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Water bridges: C:E.66, B:S.117, B:R.124 Hydrogen bonds: B:S.117, B:S.117 Salt bridges: B:R.170 PO4.44: 4 residues within 4Å: Chain C: G.116, S.117, R.170, R.242 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.117, C:R.242 Water bridges: C:S.117, C:R.124, A:E.66 Salt bridges: C:R.170

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

DAO.17: 3 residues within 4Å: Chain A: L.336 Ligands: FTT.30, FTT.54 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.336 DAO.23: 2 residues within 4Å: Ligands: FTT.20, FTT.21 No protein-ligand interaction detected (PLIP) DAO.29: 1 residues within 4Å: Ligands: FTT.26 No protein-ligand interaction detected (PLIP) DAO.35: 2 residues within 4Å: Chain B: F.23 Ligands: FTT.34 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.23 DAO.40: 2 residues within 4Å: Ligands: FTT.37, C8E.43 No protein-ligand interaction detected (PLIP) DAO.52: 3 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO-GMH.4, FTT.47, FTT.49 No protein-ligand interaction detected (PLIP) DAO.53: 4 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO-GMH.4, FTT.47, FTT.48, FTT.50 No protein-ligand interaction detected (PLIP) DAO.58: 3 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO.5, FTT.55, FTT.56 No protein-ligand interaction detected (PLIP)

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

KDO.18: 9 residues within 4Å: Chain A: K.152, E.159, D.160, K.198, R.199, T.200, S.201 Ligands: GP1-Z9M-KDO.2, GP1-Z9M-KDO.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.152, A:E.159, A:D.160, A:S.201 Salt bridges: A:K.152 KDO.33: 9 residues within 4Å: Chain B: K.152, E.159, D.160, K.198, R.199, T.200, S.201 Ligands: GP1-Z9M-KDO.3, GP1-Z9M-KDO.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.152, B:E.159, B:D.160, B:S.201 Salt bridges: B:K.152

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

FTT.19: 2 residues within 4Å: Ligands: GP1-Z9M-KDO.1, FTT.20 Ligand excluded by PLIP FTT.20: 5 residues within 4Å: Ligands: GP1-Z9M-KDO.1, GP1-Z9M-KDO.1, FTT.19, DAO.23, MYR.24 Ligand excluded by PLIP FTT.21: 7 residues within 4Å: Chain A: F.255, Q.275, K.277 Ligands: GP1-Z9M-KDO.1, C8E.8, DAO.23, MYR.24 Ligand excluded by PLIP FTT.22: 1 residues within 4Å: Ligands: GP1-Z9M-KDO.1 Ligand excluded by PLIP FTT.25: 10 residues within 4Å: Chain A: Y.90, Y.149, G.151 Chain B: G.19, H.21, F.23, T.308, G.337, L.338 Ligands: GP1-Z9M-KDO.2 Ligand excluded by PLIP FTT.26: 6 residues within 4Å: Chain A: Y.149, D.174 Ligands: GP1-Z9M-KDO.2, GP1-Z9M-KDO.2, FTT.27, DAO.29 Ligand excluded by PLIP FTT.27: 10 residues within 4Å: Chain A: F.88, A.129, V.147, Y.149, D.174, V.176, R.213 Ligands: GP1-Z9M-KDO.2, FTT.26, MYR.28 Ligand excluded by PLIP FTT.30: 4 residues within 4Å: Chain A: V.310, L.336 Ligands: GP1-Z9M-KDO-KDO.5, DAO.17 Ligand excluded by PLIP FTT.34: 3 residues within 4Å: Chain B: F.23 Ligands: GP1-Z9M-KDO.2, DAO.35 Ligand excluded by PLIP FTT.36: 12 residues within 4Å: Chain B: Y.90, Y.149, G.151 Chain C: G.19, H.21, F.23, L.336, G.337, L.338 Ligands: GP1-Z9M-KDO.3, FTT.37, C8E.43 Ligand excluded by PLIP FTT.37: 7 residues within 4Å: Chain B: Y.149, D.174 Ligands: GP1-Z9M-KDO.3, GP1-Z9M-KDO.3, FTT.36, FTT.38, DAO.40 Ligand excluded by PLIP FTT.38: 12 residues within 4Å: Chain B: F.88, A.129, T.130, Y.131, V.147, Y.149, D.174, V.176, R.213 Ligands: GP1-Z9M-KDO.3, FTT.37, MYR.39 Ligand excluded by PLIP FTT.46: 3 residues within 4Å: Chain C: F.23 Ligands: GP1-Z9M-KDO.3, C8E.43 Ligand excluded by PLIP FTT.47: 7 residues within 4Å: Chain C: Y.217 Ligands: GP1-Z9M-KDO-KDO-GMH.4, GP1-Z9M-KDO-KDO-GMH.4, C8E.41, FTT.49, DAO.52, DAO.53 Ligand excluded by PLIP FTT.48: 2 residues within 4Å: Ligands: GP1-Z9M-KDO-KDO-GMH.4, DAO.53 Ligand excluded by PLIP FTT.49: 7 residues within 4Å: Chain C: Y.217, Q.236, Y.238 Ligands: GP1-Z9M-KDO-KDO-GMH.4, FTT.47, MYR.51, DAO.52 Ligand excluded by PLIP FTT.50: 10 residues within 4Å: Chain C: F.145, A.146, G.177, G.178, S.196, R.213, E.215 Ligands: GP1-Z9M-KDO-KDO-GMH.4, DAO.53, MYR.57 Ligand excluded by PLIP FTT.54: 9 residues within 4Å: Chain A: H.21, F.23, G.337 Chain C: Y.90, Y.149, G.151 Ligands: GP1-Z9M-KDO-KDO.5, DAO.17, FTT.55 Ligand excluded by PLIP FTT.55: 7 residues within 4Å: Chain C: Y.149, D.174 Ligands: GP1-Z9M-KDO-KDO.5, GP1-Z9M-KDO-KDO.5, FTT.54, FTT.56, DAO.58 Ligand excluded by PLIP FTT.56: 12 residues within 4Å: Chain C: F.88, A.129, Y.131, V.147, Q.148, Y.149, D.174, R.213 Ligands: GP1-Z9M-KDO-KDO.5, FTT.55, MYR.57, DAO.58 Ligand excluded by PLIP

5 x MYR: MYRISTIC ACID(Non-covalent)

MYR.24: 3 residues within 4Å: Chain A: F.255 Ligands: FTT.20, FTT.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.255 MYR.28: 2 residues within 4Å: Chain A: R.213 Ligands: FTT.27 No protein-ligand interaction detected (PLIP) MYR.39: 2 residues within 4Å: Chain B: R.213 Ligands: FTT.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.213 MYR.51: 6 residues within 4Å: Chain C: T.192, Y.217, T.218, Y.234, Q.236 Ligands: FTT.49 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.234, C:Q.236 Hydrogen bonds: C:Y.238 MYR.57: 5 residues within 4Å: Chain C: V.147, V.176, R.213 Ligands: FTT.50, FTT.56 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.147, C:V.176 Hydrogen bonds: C:R.213 Water bridges: C:V.176

1 x CA: CALCIUM ION(Non-covalent)

CA.45: 4 residues within 4Å: Chain C: N.210, N.239, N.250 Ligands: GP1-Z9M-KDO-KDO-GMH.4 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.210, H2O.29

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
D

B
E

C
F

Membrane

We predict this structure to be a membrane protein.
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OMPC PORIN

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