SMTL ID : 4of9.1

Structure of K42N variant of sperm whale myoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

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

HEM.1: 17 residues within 4Å: Chain A: T.39, N.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 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:T.67, A:V.68, A:V.68, A:A.71, A:L.89, A:H.97, A:I.99, A:Y.103, A:L.104, A:I.107, A:F.138, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:R.45, A:H.64 Salt bridges: A:R.45, A:H.93, A:H.97 pi-Stacking: A:H.97 Metal complexes: A:H.93, H2O.1

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

SO4.2: 3 residues within 4Å: Chain A: T.51, E.52, A.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.52, A:A.53 SO4.3: 4 residues within 4Å: Chain A: R.45, K.63, H.64, T.67 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.67, A:T.67 Water bridges: A:R.45 Salt bridges: A:R.45, A:K.63, A:H.64 SO4.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.87 SO4.5: 2 residues within 4Å: Chain A: S.3, G.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:S.3 Water bridges: A:G.5

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: Q.26, K.56, A.57, S.58, E.59, K.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.26, A:E.59 Water bridges: A:K.62 EDO.7: 5 residues within 4Å: Chain A: A.94, T.95, L.149, G.150, Y.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.150 EDO.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-11-26

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin