SMTL ID : 7vdn.1

High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.93 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: A.57, S.58, E.59, D.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.57, A:E.59, A:D.60 SO4.2: 2 residues within 4Å: Chain A: Q.26, K.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.26 Water bridges: A:K.62 Salt bridges: A:K.62 SO4.3: 2 residues within 4Å: Chain A: R.45, K.63 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.45, A:R.45, A:R.45, A:T.67 Salt bridges: A:R.45, A:K.63

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

HEM.4: 18 residues within 4Å: Chain A: T.39, K.42, F.43, R.45, H.64, T.67, V.68, A.71, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: CMO.5 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:T.39, A:F.43, A:F.43, A:F.43, A:T.67, A:V.68, A:A.71, A:L.89, A:H.97, A:I.99, A:Y.103, A:I.107, A:F.138, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:R.45, A:R.45 Salt bridges: A:R.45, A:H.64, A:H.93, A:K.96, A:H.97 pi-Stacking: A:H.93, A:H.97 Metal complexes: A:H.93, CMO.5

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

CMO.5: 5 residues within 4Å: Chain A: F.43, H.64, V.68, H.93 Ligands: HEM.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato-Tomita, A. et al., X-ray fluorescence holography of biological metal sites: Application to myoglobin. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-09-14

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

Related Entries With Identical Sequence