SMTL ID : 6m9a.1

Bordetella pertussis globin coupled sensor regulatory domain (BpeGReg)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: F.52, M.56, A.62, F.65, L.66, L.70, K.74, L.75, S.78, M.79, W.82, V.105, V.108, H.109, I.112, I.114, L.118, V.119, G.122, A.123 Ligands: PEO.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.52, A:F.52, A:A.62, A:F.65, A:L.66, A:L.70, A:W.82, A:V.105, A:V.108, A:I.112, A:I.114, A:L.118, A:V.119 Salt bridges: A:K.74, A:K.74 pi-Stacking: A:F.52 Metal complexes: A:H.109 HEM.4: 21 residues within 4Å: Chain B: F.52, M.56, A.62, F.65, L.66, L.70, K.74, L.75, S.78, M.79, W.82, V.105, V.108, H.109, I.112, I.114, L.118, V.119, G.122, A.123 Ligands: PEO.5 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:F.52, B:F.52, B:A.62, B:F.65, B:L.66, B:L.70, B:W.82, B:V.105, B:V.108, B:I.112, B:I.114, B:L.118, B:V.119 Salt bridges: B:K.74, B:K.74 pi-Stacking: B:F.52 Metal complexes: B:H.109 HEM.7: 19 residues within 4Å: Chain C: F.52, M.56, A.62, F.65, L.70, K.74, L.75, S.78, M.79, W.82, V.105, V.108, H.109, I.112, I.114, L.118, V.119, A.123, V.160 17 PLIP interactions: 16 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:F.52, C:A.62, C:F.65, C:L.70, C:L.75, C:L.75, C:W.82, C:V.105, C:V.108, C:I.114, C:L.118, C:L.118, C:V.119, C:V.160 Salt bridges: C:K.74 Metal complexes: C:H.109, H2O.7 HEM.9: 19 residues within 4Å: Chain D: F.52, M.56, A.62, F.65, L.70, K.74, L.75, S.78, M.79, W.82, V.105, V.108, H.109, I.112, I.114, L.118, V.119, A.123, V.160 17 PLIP interactions: 16 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:F.52, D:A.62, D:F.65, D:L.70, D:L.75, D:L.75, D:W.82, D:V.105, D:V.108, D:I.114, D:L.118, D:L.118, D:V.119, D:V.160 Salt bridges: D:K.74 Metal complexes: D:H.109, H2O.9 HEM.11: 22 residues within 4Å: Chain E: F.52, M.56, A.62, F.65, L.66, L.70, K.74, L.75, S.78, M.79, W.82, K.104, V.105, V.108, H.109, R.111, I.114, L.118, V.119, G.122, A.123 Ligands: PEO.12 16 PLIP interactions: 16 interactions with chain E, Hydrophobic interactions: E:F.52, E:F.65, E:L.66, E:L.66, E:L.70, E:L.75, E:W.82, E:W.82, E:V.105, E:V.108, E:I.114, E:L.118 Hydrogen bonds: E:R.111 Salt bridges: E:K.74, E:K.104 Metal complexes: E:H.109 HEM.14: 22 residues within 4Å: Chain F: F.52, M.56, A.62, F.65, L.66, L.70, K.74, L.75, S.78, M.79, W.82, K.104, V.105, V.108, H.109, R.111, I.114, L.118, V.119, G.122, A.123 Ligands: PEO.15 16 PLIP interactions: 16 interactions with chain F, Hydrophobic interactions: F:F.52, F:F.65, F:L.66, F:L.66, F:L.70, F:L.75, F:W.82, F:W.82, F:V.105, F:V.108, F:I.114, F:L.118 Hydrogen bonds: F:R.111 Salt bridges: F:K.74, F:K.104 Metal complexes: F:H.109

4 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.2: 4 residues within 4Å: Chain A: Y.53, L.75, H.109 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.53 Water bridges: A:Y.53, A:Y.53 PEO.5: 4 residues within 4Å: Chain B: Y.53, L.75, H.109 Ligands: HEM.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.53, B:Y.53 PEO.12: 4 residues within 4Å: Chain E: Y.53, L.75, H.109 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.53 PEO.15: 4 residues within 4Å: Chain F: Y.53, L.75, H.109 Ligands: HEM.14 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.53, F:Y.53

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: D.135 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.135, H2O.2, H2O.3 CA.6: 1 residues within 4Å: Chain B: D.135 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.135, H2O.5, H2O.5 CA.8: 1 residues within 4Å: Chain C: D.135 No protein-ligand interaction detected (PLIP) CA.10: 1 residues within 4Å: Chain D: D.135 No protein-ligand interaction detected (PLIP) CA.13: 1 residues within 4Å: Chain E: D.135 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.135, H2O.11, H2O.11, H2O.12 CA.16: 1 residues within 4Å: Chain F: D.135 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.135, H2O.13, H2O.13, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rivera, S. et al., Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled Sensors. Inorg Chem (2018)

Release Date

2018-11-14

Peptides

Signaling protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
C

D
C

E
B

F
B

Signaling protein