SMTL ID : 2fgq.1

High resolution X-ray structure of Omp32 in complex with malate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 8 residues within 4Å: Chain A: L.6 Chain B: V.4 Chain C: V.4, L.6, L.41, F.71 Ligands: BOG.8, BOG.15 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.6, C:L.41, C:F.71 Water bridges: B:L.6 BOG.8: 8 residues within 4Å: Chain A: V.4, L.6, L.41, F.71 Chain B: L.6 Chain C: V.4 Ligands: BOG.1, BOG.15 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.6, A:L.41, A:F.71 Water bridges: C:L.6 BOG.15: 8 residues within 4Å: Chain A: V.4 Chain B: V.4, L.6, L.41, F.71 Chain C: L.6 Ligands: BOG.1, BOG.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.6, B:L.41, B:F.71 Water bridges: A:L.6

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: L.29, D.64, G.309 Chain C: N.136, E.158 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:L.29, A:D.64, A:G.309, C:E.158, H2O.1 CA.3: 8 residues within 4Å: Chain A: G.70, F.71 Chain B: G.70, F.71 Chain C: G.70, F.71 Ligands: CA.10, CA.17 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:F.71, B:F.71, C:F.71 CA.4: 6 residues within 4Å: Chain A: G.54, F.55, W.56, R.76, T.78, S.80 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.80 CA.9: 5 residues within 4Å: Chain A: N.136, E.158 Chain B: L.29, D.64, G.309 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:L.29, B:D.64, B:G.309, A:E.158, H2O.15 CA.10: 8 residues within 4Å: Chain A: G.70, F.71 Chain B: G.70, F.71 Chain C: G.70, F.71 Ligands: CA.3, CA.17 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Metal complexes: A:F.71, B:F.71, C:F.71 CA.11: 6 residues within 4Å: Chain B: G.54, F.55, W.56, R.76, T.78, S.80 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.80 CA.16: 5 residues within 4Å: Chain B: N.136, E.158 Chain C: L.29, D.64, G.309 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.158, C:L.29, C:D.64, C:G.309, H2O.30 CA.17: 8 residues within 4Å: Chain A: G.70, F.71 Chain B: G.70, F.71 Chain C: G.70, F.71 Ligands: CA.3, CA.10 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:F.71, A:F.71, B:F.71 CA.18: 6 residues within 4Å: Chain C: G.54, F.55, W.56, R.76, T.78, S.80 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.80

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

SO4.5: 4 residues within 4Å: Chain A: E.254, K.256, V.279, R.329 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.256, A:K.256, A:R.329, A:R.329 Salt bridges: A:K.256, A:R.329 SO4.6: 3 residues within 4Å: Chain A: S.35, R.38 Ligands: MLT.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.75 Water bridges: A:T.36, A:R.38, A:R.38, A:S.108, A:S.108 Salt bridges: A:R.38 SO4.12: 4 residues within 4Å: Chain B: E.254, K.256, V.279, R.329 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.256, B:K.256, B:R.329, B:R.329 Salt bridges: B:K.256, B:R.329 SO4.13: 3 residues within 4Å: Chain B: S.35, R.38 Ligands: MLT.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.75 Water bridges: B:T.36, B:R.38, B:R.38, B:S.108, B:S.108 Salt bridges: B:R.38 SO4.19: 4 residues within 4Å: Chain C: E.254, K.256, V.279, R.329 6 PLIP interactions: 6 interactions with chain C Water bridges: C:K.256, C:K.256, C:R.329, C:R.329 Salt bridges: C:K.256, C:R.329 SO4.20: 3 residues within 4Å: Chain C: S.35, R.38 Ligands: MLT.21 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.75 Water bridges: C:T.36, C:R.38, C:R.38, C:S.108, C:S.108 Salt bridges: C:R.38

3 x MLT: D-MALATE(Non-covalent)

MLT.7: 7 residues within 4Å: Chain A: T.36, R.75, L.94, T.102, A.109, R.133 Ligands: SO4.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.109 Hydrogen bonds: A:R.75, A:R.133, A:R.133 Water bridges: A:T.36, A:R.38 Salt bridges: A:R.38, A:R.75, A:R.133 MLT.14: 7 residues within 4Å: Chain B: T.36, R.75, L.94, T.102, A.109, R.133 Ligands: SO4.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.109 Hydrogen bonds: B:R.75, B:R.133, B:R.133 Water bridges: B:T.36, B:R.38 Salt bridges: B:R.38, B:R.75, B:R.133 MLT.21: 7 residues within 4Å: Chain C: T.36, R.75, L.94, T.102, A.109, R.133 Ligands: SO4.20 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.109 Hydrogen bonds: C:R.75, C:R.133, C:R.133 Water bridges: C:T.36, C:R.38 Salt bridges: C:R.38, C:R.75, C:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zachariae, U. et al., High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin omp32. J.Biol.Chem. (2006)

Release Date

2006-01-31

Peptides

Outer membrane porin protein 32: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

C
X

Membrane

We predict this structure to be a membrane protein.
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Outer membrane porin protein 32

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