SMTL ID : 1w92.1

The structure of carbomonoxy murine neuroglobin reveals a heme- sliding mechanism for affinity regulation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: L.41, F.42, Y.44, H.64, K.67, V.68, V.71, L.92, K.95, H.96, V.101, R.102, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.2 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.41, A:F.42, A:F.42, A:F.42, A:V.68, A:V.71, A:V.71, A:L.92, A:V.101, A:V.101, A:F.106, A:V.109, A:Y.137, A:V.140 Water bridges: A:H.64, A:Y.88 Salt bridges: A:K.67, A:K.67, A:K.95 pi-Stacking: A:H.64 Metal complexes: A:H.96, CMO.2 HEM.3: 19 residues within 4Å: Chain B: L.41, F.42, Y.44, H.64, K.67, V.68, V.71, L.92, K.95, H.96, V.101, R.102, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.4 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.41, B:F.42, B:F.42, B:F.42, B:V.68, B:V.71, B:V.71, B:L.92, B:V.101, B:V.101, B:F.106, B:V.109, B:Y.137, B:V.140 Water bridges: B:H.64, B:Y.88 Salt bridges: B:K.67, B:K.67, B:K.95 pi-Stacking: B:H.64 Metal complexes: B:H.96, CMO.4 HEM.5: 19 residues within 4Å: Chain C: L.41, F.42, Y.44, H.64, K.67, V.68, V.71, L.92, K.95, H.96, V.101, R.102, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.6 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:L.41, C:F.42, C:F.42, C:F.42, C:V.68, C:V.71, C:V.71, C:L.92, C:V.101, C:V.101, C:F.106, C:V.109, C:Y.137, C:V.140 Water bridges: C:H.64, C:Y.88 Salt bridges: C:K.67, C:K.67, C:K.95 pi-Stacking: C:H.64 Metal complexes: C:H.96, CMO.6 HEM.7: 19 residues within 4Å: Chain D: L.41, F.42, Y.44, H.64, K.67, V.68, V.71, L.92, K.95, H.96, V.101, R.102, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.8 24 PLIP interactions: 23 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:L.41, D:F.42, D:F.42, D:F.42, D:V.68, D:V.71, D:V.71, D:L.92, D:V.101, D:V.101, D:F.106, D:V.109, D:Y.137, D:V.140 Hydrogen bonds: D:Y.44 Water bridges: D:H.64, D:Y.88, D:Y.88 Salt bridges: D:K.67, D:K.67, D:K.95 pi-Stacking: D:H.64 Metal complexes: D:H.96, CMO.8 HEM.9: 19 residues within 4Å: Chain E: L.41, F.42, Y.44, H.64, K.67, V.68, V.71, L.92, K.95, H.96, V.101, R.102, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.10 24 PLIP interactions: 23 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:L.41, E:F.42, E:F.42, E:F.42, E:V.68, E:V.71, E:V.71, E:L.92, E:V.101, E:V.101, E:F.106, E:V.109, E:Y.137, E:V.140 Hydrogen bonds: E:Y.44 Water bridges: E:H.64, E:Y.88, E:Y.88 Salt bridges: E:K.67, E:K.67, E:K.95 pi-Stacking: E:H.64 Metal complexes: E:H.96, CMO.10 HEM.11: 19 residues within 4Å: Chain F: L.41, F.42, Y.44, H.64, K.67, V.68, V.71, L.92, K.95, H.96, V.101, R.102, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.12 24 PLIP interactions: 23 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:L.41, F:F.42, F:F.42, F:F.42, F:V.68, F:V.71, F:V.71, F:L.92, F:V.101, F:V.101, F:F.106, F:V.109, F:Y.137, F:V.140 Hydrogen bonds: F:Y.44 Water bridges: F:H.64, F:Y.88, F:Y.88 Salt bridges: F:K.67, F:K.67, F:K.95 pi-Stacking: F:H.64 Metal complexes: F:H.96, CMO.12

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

CMO.2: 5 residues within 4Å: Chain A: F.28, H.64, V.68, H.96 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.4: 5 residues within 4Å: Chain B: F.28, H.64, V.68, H.96 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.6: 5 residues within 4Å: Chain C: F.28, H.64, V.68, H.96 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) CMO.8: 5 residues within 4Å: Chain D: F.28, H.64, V.68, H.96 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) CMO.10: 5 residues within 4Å: Chain E: F.28, H.64, V.68, H.96 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) CMO.12: 5 residues within 4Å: Chain F: F.28, H.64, V.68, H.96 Ligands: HEM.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vallone, B. et al., The Structure of Carbonmonoxy Neuroglobin Reveals a Heme-Sliding Mechanism for Control of Ligand Affinity. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-11-02

Peptides

NEUROGLOBIN: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

NEUROGLOBIN

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