SMTL ID : 2vv8.1

Co-bound structure of bjFixLH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 25 residues within 4Å: Chain A: I.7, I.9, V.38, L.41, M.42, D.46, H.50, Y.53, I.54, R.56, Y.57, P.63, H.64, I.65, I.66, R.70, V.72, T.73, M.84, L.86, I.88, F.99, T.100, G.101 Ligands: CMO.2 28 PLIP interactions: 28 interactions with chain A, Hydrophobic interactions: A:I.7, A:I.9, A:V.38, A:L.41, A:M.42, A:Y.53, A:Y.53, A:Y.53, A:Y.53, A:I.54, A:Y.57, A:Y.57, A:H.64, A:I.65, A:I.66, A:V.72, A:I.88, A:F.99 Hydrogen bonds: A:H.64, A:I.65, A:I.66 Water bridges: A:Y.53, A:H.64 Salt bridges: A:R.56, A:H.64, A:H.64, A:R.70 Metal complexes: A:H.50 HEM.3: 22 residues within 4Å: Chain B: I.7, I.9, V.38, L.41, M.42, D.46, H.50, Y.53, Y.57, P.63, H.64, I.65, I.66, R.70, V.72, T.73, M.84, L.86, I.88, F.99, G.101 Ligands: CMO.4 24 PLIP interactions: 23 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:I.7, B:I.9, B:V.38, B:L.41, B:Y.53, B:Y.53, B:Y.53, B:Y.53, B:Y.57, B:H.64, B:I.65, B:I.66, B:V.72, B:I.88, B:F.99 Hydrogen bonds: B:H.64, B:H.64, B:I.65, B:I.66 Water bridges: B:Y.53 Salt bridges: B:H.64, B:R.70 Metal complexes: B:H.50, CMO.4 HEM.5: 24 residues within 4Å: Chain C: I.7, I.9, V.38, L.41, M.42, D.46, H.50, Y.53, I.54, Y.57, P.63, H.64, I.65, I.66, R.70, V.72, T.73, M.84, L.86, I.88, F.99, T.100, G.101 Ligands: CMO.6 29 PLIP interactions: 28 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.7, C:I.9, C:V.38, C:L.41, C:M.42, C:Y.53, C:Y.53, C:Y.53, C:I.54, C:Y.57, C:H.64, C:I.65, C:I.65, C:I.66, C:V.72, C:L.86, C:I.88, C:F.99 Hydrogen bonds: C:H.64, C:I.65, C:I.66 Water bridges: C:Y.53, C:H.64 Salt bridges: C:H.64, C:H.64, C:R.70 pi-Stacking: C:H.50 Metal complexes: C:H.50, CMO.6 HEM.10: 24 residues within 4Å: Chain D: I.7, I.9, V.38, L.41, M.42, D.46, H.50, Y.53, I.54, Y.57, P.63, H.64, I.65, I.66, R.70, V.72, T.73, M.84, L.86, I.88, F.99, T.100, G.101 Ligands: CMO.11 24 PLIP interactions: 23 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:I.7, D:I.9, D:V.38, D:L.41, D:M.42, D:Y.53, D:Y.53, D:Y.53, D:I.54, D:Y.57, D:Y.57, D:H.64, D:I.65, D:I.66, D:V.72, D:I.88, D:F.99 Hydrogen bonds: D:H.64, D:I.65, D:I.66 Salt bridges: D:H.64, D:R.70 Metal complexes: D:H.50, CMO.11

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.2: 4 residues within 4Å: Chain A: I.65, L.86, I.88 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.4: 5 residues within 4Å: Chain B: H.50, I.65, L.86, I.88 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.6: 5 residues within 4Å: Chain C: H.50, I.65, L.86, I.88 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) CMO.11: 5 residues within 4Å: Chain D: H.50, I.65, L.86, I.88 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain C: L.31, E.32, I.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.34

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

CL.8: 7 residues within 4Å: Chain C: I.68, G.69, H.85, S.87 Chain D: Q.92, S.93, G.94 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: H.85, R.104 Chain D: G.94 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ayers, R.A. et al., Changes in Quaternary Structure in the Signaling Mechanisms of Pas Domains. Biochemistry (2008)

Release Date

2008-11-04

Peptides

SENSOR PROTEIN FIXL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SENSOR PROTEIN FIXL

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