SMTL ID : 6i40.1

Crystal structure of murine neuroglobin bound to CO at 15K under illumination using optical fiber

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: L.38, L.41, F.42, Y.44, H.64, V.68, V.71, Y.88, L.92, H.96, V.101, S.105, F.106, V.109, Y.137, V.140, M.144 Ligands: CMO.2, FMT.5, ACT.8 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.38, 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:L.92, A:V.101, A:F.106, A:F.106, A:V.109, A:Y.137, A:V.140 Water bridges: A:H.64, A:K.67 Salt bridges: A:K.95 pi-Stacking: A:H.64 Metal complexes: A:H.96

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

CMO.2: 4 residues within 4Å: Chain A: F.28, H.64, V.68 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: E.5, I.9, A.132, R.135, L.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.5, A:L.136 FMT.4: 4 residues within 4Å: Chain A: S.107, G.110, E.111, S.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.134 FMT.5: 7 residues within 4Å: Chain A: L.38, L.41, G.100, V.101, R.102, S.105 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.102, A:S.105

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

ACT.6: 6 residues within 4Å: Chain A: S.83, S.84, L.85, E.86, E.87, Y.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.87 Hydrogen bonds: A:Y.88 ACT.7: 3 residues within 4Å: Chain A: L.62, D.63, R.66 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.66 ACT.8: 2 residues within 4Å: Chain A: K.67 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.67 ACT.9: 3 residues within 4Å: Chain A: T.90, S.91, R.94 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.91 Salt bridges: A:R.94

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: S.17, P.20, D.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.17, A:D.73 Water bridges: A:S.17, A:S.17 GOL.11: 6 residues within 4Å: Chain A: R.18, S.19, P.20, L.21, E.22, R.66 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.21, A:E.22, A:E.22, A:E.22, A:R.66, A:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ardiccioni, C. et al., Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. Iucrj (2019)

Release Date

2019-09-11

Peptides

Neuroglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neuroglobin

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