SMTL ID : 5kd1.1 (1 other biounit)

Sperm whale myoglobin H64A with nitrosoamphetamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: T.39, K.42, F.43, R.45, T.67, V.68, A.71, L.72, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: 3QM.6 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:T.67, A:V.68, A:L.89, 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:P.88, A:S.92 Salt bridges: A:R.45, A:H.93, A:H.97 pi-Stacking: A:H.93, A:H.93, A:H.97 Metal complexes: A:H.93

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: 2 residues within 4Å: Chain A: A.15, K.16 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.15, A:K.16 Salt bridges: A:K.16 SO4.4: 1 residues within 4Å: Chain A: K.87 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.87 SO4.5: 3 residues within 4Å: Chain A: S.3, G.5, E.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:S.3 Water bridges: A:G.5

1 x 3QM: [(2R)-2-nitrosopropyl]benzene(Non-covalent)

3QM.6: 7 residues within 4Å: Chain A: L.29, F.43, A.64, T.67, V.68, I.107 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.29, A:F.43, A:A.64, A:T.67, A:I.107

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: A.57, S.58, E.59, D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.59, A:D.60 GOL.8: 2 residues within 4Å: Chain A: R.31, H.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.31, A:R.31, A:H.113 GOL.9: 7 residues within 4Å: Chain A: G.121, N.122, F.123, G.124, A.125, D.126, A.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.124, A:D.126, A:A.127 Water bridges: A:N.122 GOL.10: 7 residues within 4Å: Chain A: K.78, H.81, H.82, E.83, A.84, E.85 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.78, A:E.83, A:A.84, A:E.85 Water bridges: A:H.81 GOL.11: 2 residues within 4Å: Chain A: H.81 Ligands: GOL.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Nitrosoamphetamine binding to myoglobin and hemoglobin: Crystal structure of the H64A myoglobin-nitrosoamphetamine adduct. Nitric Oxide (2017)

Release Date

2017-05-10

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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