SMTL ID : 7dgn.1

The Co-bound dimeric structure of K79H/G80A/H81A myoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Chain B: T.39, K.42, F.43, K.45, H.64, V.67, V.68, A.71, L.72 Ligands: O.4 21 PLIP interactions: 7 interactions with chain B, 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.43, B:F.43, B:V.68, B:V.68, B:A.71, B:L.72, A:L.89, A:L.89, A:I.99, A:I.99, A:Y.103, A:I.107, A:F.138 Salt bridges: B:K.45, A:H.93, A:H.97 Hydrogen bonds: A:S.92 Water bridges: A:P.88 pi-Stacking: A:H.97 Metal complexes: A:H.93, O.4 HEM.5: 19 residues within 4Å: Chain A: T.39, K.42, F.43, K.45, H.64, V.67, V.68, A.71, L.72 Chain B: L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: O.2 25 PLIP interactions: 15 interactions with chain B, 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.89, B:L.89, B:I.99, B:Y.103, B:Y.103, B:L.104, B:I.107, B:I.107, B:F.138, A:F.43, A:F.43, A:F.43, A:V.67, A:V.68, A:A.71, A:L.72, A:L.72 Hydrogen bonds: B:S.92 Water bridges: B:K.96 Salt bridges: B:H.93, B:H.97, A:K.45 pi-Stacking: B:H.97 Metal complexes: B:H.93, O.2

2 x O: OXYGEN ATOM(Non-covalent)

O.2: 4 residues within 4Å: Chain A: F.43, H.64, V.68 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) O.4: 3 residues within 4Å: Chain B: H.64, V.68 Ligands: HEM.1 No protein-ligand interaction detected (PLIP)

2 x CO: COBALT (II) ION(Non-covalent)

CO.3: 3 residues within 4Å: Chain A: H.82, D.141 Chain B: H.79 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.79, A:H.82, A:D.141, H2O.3 CO.6: 3 residues within 4Å: Chain A: H.79 Chain B: H.82, D.141 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.82, B:D.141, A:H.79, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagao, S. et al., Rational design of metal-binding sites in domain-swapped myoglobin dimers. J.Inorg.Biochem. (2021)

Release Date

2021-02-17

Peptides

Myoglobin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Myoglobin

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