SMTL ID : 5yce.1

Sperm whale myoglobin swMb

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.77 Å

Oligo State

monomer

Ligands

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

HEM.1: 17 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 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:T.40, A:F.44, A:F.44, A:F.44, A:F.44, A:T.68, A:V.69, A:A.72, A:L.90, A:H.98, A:I.100, A:Y.104, A:I.108, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:D.45, A:R.46, A:R.46 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.65, A:H.98 Metal complexes: A:H.94, H2O.3

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

SO4.2: 4 residues within 4Å: Chain A: A.58, S.59, E.60, D.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.60, A:D.61 SO4.3: 3 residues within 4Å: Chain A: Q.27, K.57, K.63 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.27 Water bridges: A:K.57, A:K.57, A:K.57, A:K.57 Salt bridges: A:K.57, A:K.63 SO4.4: 4 residues within 4Å: Chain A: R.46, K.64, H.65, T.68 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.68 Water bridges: A:R.46, A:R.46, A:K.64 Salt bridges: A:R.46, A:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Isogai, Y. et al., Tracing whale myoglobin evolution by resurrecting ancient proteins. Sci Rep (2018)

Release Date

2018-09-19

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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