SMTL ID : 2vly.1

Crystal structure of myoglobin compound III (radiation-induced)

Coordinates

PDB Format Compare

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: OXY.2 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:V.67, A:V.68, A:A.71, A:L.89, A:L.89, A:I.99, A:I.99, A:I.99, A:Y.103, A:I.107, 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.64, A:H.97 pi-Cation interactions: A:H.93 Metal complexes: A:H.93

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 5 residues within 4Å: Chain A: F.43, H.64, V.68, H.93 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.31, H.113, S.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.31, A:S.117, A:S.117 Water bridges: A:S.117 GOL.6: 7 residues within 4Å: Chain A: R.31, G.35, H.36, D.109, A.110, H.113 Ligands: PEO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.31, A:D.109 Water bridges: A:G.35

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

PEO.7: 7 residues within 4Å: Chain A: R.31, L.32, H.36, F.106, D.109, A.110 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.106 PEO.8: 3 residues within 4Å: Chain A: S.3, D.4, G.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.3, A:G.5 Water bridges: A:S.3, A:D.4, A:D.4

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

Related Entries With Identical Sequence