SMTL ID : 2vm0.1

Crystal structure of radiation-induced myoglobin compound II generated after annealing of peroxymyoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: T.39, K.42, F.43, K.45, H.64, V.67, V.68, A.71, L.72, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: OH.2 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.39, A:F.43, A:F.43, A:F.43, A:V.67, A:V.68, A:L.89, A:I.99, A:Y.103, A:I.107, A:F.138, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:H.64 Salt bridges: A:K.45, A:H.93, A:H.97 pi-Stacking: A:H.93, A:H.97 Metal complexes: A:H.93, OH.2

1 x OH: HYDROXIDE ION(Non-covalent)

OH.2: 4 residues within 4Å: Chain A: F.43, H.64, V.68 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.64

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

SO4.3: 3 residues within 4Å: Chain A: K.50, T.51, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.52 Water bridges: A:T.51, A:A.53 SO4.4: 1 residues within 4Å: Chain A: G.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.31, H.36, D.109, A.110, H.113 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.31, A:R.31, A:H.36 Water bridges: A:D.109, A:A.110, A:H.113

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

PEO.6: 5 residues within 4Å: Chain A: G.1, L.2, W.7, K.79, L.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.2, A:K.79 PEO.7: 3 residues within 4Å: Chain A: E.59, K.62, K.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.59, A:K.63 PEO.8: 4 residues within 4Å: Chain A: K.16, A.19, H.24, H.119 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hersleth, H.-P. et al., The Crystal Structure of Peroxymyoglobin Generated Through Cryoradiolytic Reduction of Myoglobin Compound III During Data Collection. Biochem.J. (2008)

Release Date

2008-01-29

Peptides

MYOGLOBIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MYOGLOBIN

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