SMTL ID : 6h6j.1

Carbomonoxy murine neuroglobin Gly-loop mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: L.39, L.42, P.59, H.64, K.67, V.68, V.71, Y.88, L.92, K.95, H.96, V.99, V.101, F.106, V.109 Ligands: CMO.2 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.39, A:L.42, A:P.59, A:K.67, A:K.67, A:V.71, A:V.71, A:V.71, A:L.92, A:L.92, A:K.95, A:V.99, A:V.101, A:F.106, A:V.109 Salt bridges: A:K.95 Metal complexes: A:H.96, CMO.2

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

CMO.2: 5 residues within 4Å: Chain A: F.43, H.64, V.68, H.96 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

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

SO4.3: 1 residues within 4Å: Chain A: R.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 SO4.10: 3 residues within 4Å: Chain A: R.4, E.8, R.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.8 Salt bridges: A:R.4, A:R.11

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain A: W.14, S.18, P.21, R.66, M.69, L.70, D.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.18, A:R.66, A:R.66, A:M.69

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: H.1, V.79, E.80, D.81, L.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.1, A:L.82, A:R.135 Water bridges: A:H.1 GOL.6: 2 residues within 4Å: Chain A: V.27, Y.115 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: K.67, L.70, V.71, Y.88 No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain A: R.31, Y.115, K.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.31, A:K.119 PEG.9: 4 residues within 4Å: Chain A: R.102, L.103, S.104, W.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.102, A:L.103, A:W.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Exertier, C. et al., Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating. Sci Rep (2019)

Release Date

2019-04-10

Peptides

Neuroglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuroglobin