SMTL ID : 8esu.1

Myoglobin variant Mb-imi complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, T.68, A.69, A.72, L.73, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: IMD.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:A.69, A:A.72, A:L.90, A:I.100, A:I.100, A:Y.104, A:I.108, A:I.108, A:F.139, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:P.89, A:K.97, A:K.97, A:K.97 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.98 Metal complexes: A:H.94

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 5 residues within 4Å: Chain A: L.30, F.44, G.65, A.69 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:F.44

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

SO4.3: 2 residues within 4Å: Chain A: S.4, E.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.5 Water bridges: A:G.6, A:G.6 SO4.4: 3 residues within 4Å: Chain A: R.32, K.35, H.114 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.36 Salt bridges: A:R.32, A:K.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, D. et al., Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nat Commun (2023)

Release Date

2023-12-06

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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