SMTL ID : 5u1h.5 (4 other biounits)

Crystal structure of the C-terminal peptidoglycan binding domain of OprF (PA1777) from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x 7QA: (2R,6S)-2-amino-6-(carboxyamino)-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoic acid(Non-covalent)

7QA.1: 10 residues within 4Å: Chain A: F.19, D.20, T.53, D.54, V.56, Y.61, N.62, L.65, R.69, R.112 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.19, A:D.20, A:Y.61, A:L.65 Hydrogen bonds: A:D.20, A:D.20, A:D.54, A:D.54, A:V.56, A:V.56, A:N.62 Salt bridges: A:R.69 7QA.4: 11 residues within 4Å: Chain B: F.19, D.20, T.53, D.54, V.56, G.57, Y.61, N.62, L.65, R.69, R.112 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.19, B:F.19, B:D.20, B:Y.61, B:L.65 Hydrogen bonds: B:D.20, B:D.20, B:D.20, B:D.54, B:V.56, B:V.56, B:N.62 Salt bridges: B:R.69, B:R.112 7QA.12: 11 residues within 4Å: Chain C: F.19, D.20, T.53, D.54, V.56, G.57, Y.61, N.62, L.65, R.69, R.112 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.19, C:F.19, C:D.20, C:Y.61, C:L.65 Hydrogen bonds: C:D.20, C:D.20, C:D.20, C:D.54, C:D.54, C:V.56, C:V.56, C:N.62 Water bridges: C:T.58 Salt bridges: C:R.69, C:R.112 7QA.17: 11 residues within 4Å: Chain D: F.19, D.20, T.53, D.54, V.56, G.57, Y.61, N.62, L.65, R.69, R.112 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.19, D:F.19, D:D.20, D:Y.61, D:L.65 Hydrogen bonds: D:D.20, D:D.20, D:D.54, D:D.54, D:V.56, D:V.56, D:N.62 Salt bridges: D:R.69, D:R.112

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: K.33, N.34, D.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.37 Water bridges: A:K.33, A:K.33 Salt bridges: A:K.33 ACT.10: 1 residues within 4Å: Chain B: E.95 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.95

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: Y.42, P.43, S.44 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: Y.42, P.43, S.44 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: Y.42, P.43, S.44 Ligand excluded by PLIP

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

SO4.5: 2 residues within 4Å: Chain B: R.74, G.85 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.74, B:N.79, B:N.79 Salt bridges: B:R.74 SO4.6: 2 residues within 4Å: Chain B: A.109, R.112 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.112, B:R.112, B:R.112, B:R.112, B:R.112, B:R.112, B:R.112 Salt bridges: B:R.112 SO4.7: 4 residues within 4Å: Chain B: R.10, E.117, E.119 Chain C: R.10 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:R.10 Water bridges: B:E.117, B:E.117, A:E.115 Salt bridges: C:R.10 SO4.8: 3 residues within 4Å: Chain B: K.23, K.25, E.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.26 Water bridges: B:D.18, B:K.25, B:N.27 Salt bridges: B:K.23, B:K.25 SO4.9: 1 residues within 4Å: Chain D: S.1 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.1, D:S.1 Water bridges: B:N.2 SO4.13: 2 residues within 4Å: Chain C: T.58, D.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.59 SO4.14: 3 residues within 4Å: Chain C: S.55, V.56, G.57 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.57 SO4.15: 3 residues within 4Å: Chain B: R.10 Chain C: E.117, E.119 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Salt bridges: B:R.10 Water bridges: C:E.117, C:E.119, D:R.97 SO4.16: 3 residues within 4Å: Chain C: V.88, N.89, A.90 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.90 Water bridges: C:R.74 SO4.18: 3 residues within 4Å: Chain D: R.74, G.85, G.86 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.85 Water bridges: D:R.74 Salt bridges: D:R.74 SO4.19: 3 residues within 4Å: Chain A: R.10 Chain D: E.117, E.119 10 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A, 1 interactions with chain D Water bridges: C:R.97, C:R.97, C:E.115, C:E.115, C:E.115, A:R.10, A:Q.12, A:Q.12 Salt bridges: A:R.10 Hydrogen bonds: D:E.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, N., Crystal structure of the C-terminal peptidoglycan binding domain of OprF (PA1777) from Pseudomonas aeruginosa. To be published

Release Date

2017-01-11

Peptides

Outer membrane porin F: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Outer membrane porin F

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