SMTL ID : 2fgr.1

High resolution Xray structure of Omp32

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x ASP- ASN- TRP- GLN- ASN- GLY- THR- SER: PAP(Non-covalent)

ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1: 20 residues within 4Å: Chain A: S.3, V.4, T.5, L.6, F.7, L.41, R.42, R.285, F.332 Chain C: L.6, R.285, F.332 Ligands: ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13 18 PLIP interactions: 5 interactions with chain C, 13 interactions with chain A Hydrophobic interactions: C:L.6, C:L.6, C:F.332, A:V.4, A:V.4, A:L.6, A:L.41, A:R.285 Water bridges: C:R.285, A:F.332, A:F.332 Salt bridges: C:R.285 Hydrogen bonds: A:V.4, A:L.6, A:R.42, A:F.332, A:F.332, A:F.332 ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7: 20 residues within 4Å: Chain A: L.6, R.285, F.332 Chain B: S.3, V.4, T.5, L.6, F.7, L.41, R.42, R.285, F.332 Ligands: ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.4, B:V.4, B:L.6, B:L.41, B:R.285, A:L.6, A:L.6, A:F.332 Hydrogen bonds: B:V.4, B:L.6, B:R.42, B:F.332, B:F.332, B:F.332 Water bridges: B:F.332, B:F.332, A:R.285 Salt bridges: A:R.285 ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.13: 20 residues within 4Å: Chain B: L.6, R.285, F.332 Chain C: S.3, V.4, T.5, L.6, F.7, L.41, R.42, R.285, F.332 Ligands: ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.1, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7, ASP-ASN-TRP-GLN-ASN-GLY-THR-SER.7 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.4, C:V.4, C:L.6, C:L.41, C:R.285, B:L.6, B:L.6, B:F.332 Hydrogen bonds: C:V.4, C:L.6, C:R.42, C:F.332, C:F.332, C:F.332 Water bridges: C:F.332, C:F.332, B:R.285 Salt bridges: B:R.285

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: L.29, D.64, G.309 Chain B: N.136, E.158 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:L.29, A:D.64, A:G.309, B: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.9, CA.15 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:F.71, B:F.71, C:F.71, H2O.12, H2O.43 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:T.78 CA.8: 5 residues within 4Å: Chain B: L.29, D.64, G.309 Chain C: N.136, E.158 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:L.29, B:D.64, B:G.309, C:E.158, H2O.17 CA.9: 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.15 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:F.71, B:F.71, C:F.71, H2O.12, H2O.27 CA.10: 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:T.78 CA.14: 5 residues within 4Å: Chain A: N.136, E.158 Chain C: L.29, D.64, G.309 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:L.29, C:D.64, C:G.309, A:E.158, H2O.33 CA.15: 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.9 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:F.71, B:F.71, C:F.71, H2O.27, H2O.43 CA.16: 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:T.78

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

SO4.5: 4 residues within 4Å: Chain A: E.254, K.256, V.279, R.329 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.256, A:K.256, A:N.281 Salt bridges: A:K.256, A:R.329 SO4.6: 2 residues within 4Å: Chain A: S.35, R.38 8 PLIP interactions: 8 interactions with chain A Water bridges: A:T.36, A:R.38, A:R.38, A:R.75, A:R.75, A:R.75, A:S.108 Salt bridges: A:R.38 SO4.11: 4 residues within 4Å: Chain B: E.254, K.256, V.279, R.329 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.256, B:K.256, B:N.281 Salt bridges: B:K.256, B:R.329 SO4.12: 2 residues within 4Å: Chain B: S.35, R.38 8 PLIP interactions: 8 interactions with chain B Water bridges: B:T.36, B:R.38, B:R.38, B:R.75, B:R.75, B:R.75, B:S.108 Salt bridges: B:R.38 SO4.17: 4 residues within 4Å: Chain C: E.254, K.256, V.279, R.329 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.256, C:K.256, C:N.281 Salt bridges: C:K.256, C:R.329 SO4.18: 2 residues within 4Å: Chain C: S.35, R.38 8 PLIP interactions: 8 interactions with chain C Water bridges: C:T.36, C:R.38, C:R.38, C:R.75, C:R.75, C:R.75, C:S.108 Salt bridges: C:R.38

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
A

B
A

C
A

Membrane

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