SMTL ID : 5vzn.1

Wild-type sperm whale myoglobin with nitric oxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, H.65, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: NO.2 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:V.69, A:A.72, A:L.90, A:I.100, A:Y.104, A:I.108, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:R.46 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.94, A:H.98 Metal complexes: A:H.94, NO.2

1 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 5 residues within 4Å: Chain A: F.44, H.65, V.69, H.94 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: K.35, T.52, E.53 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.53 Water bridges: A:T.52, A:E.53, A:E.53, A:A.54 Salt bridges: A:K.35

1 x NO2: NITRITE ION(Non-covalent)

NO2.4: 5 residues within 4Å: Chain A: R.32, S.36, E.110, A.111, H.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32 Water bridges: A:A.111, A:H.114

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: V.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Biochemistry (2018)

Release Date

2018-06-06

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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