SMTL ID : 7ud8.1

Crystal structure of carbon monoxy Hemoglobin in complex with 5HMF at 1.8 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.1: 5 residues within 4Å: Chain A: L.30, H.59, V.63, H.88 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.59 OXY.4: 6 residues within 4Å: Chain B: L.29, F.43, H.64, V.68, H.93 Ligands: HEM.5 No protein-ligand interaction detected (PLIP) OXY.6: 6 residues within 4Å: Chain C: L.30, F.44, H.59, V.63, H.88 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) OXY.9: 6 residues within 4Å: Chain D: L.29, F.43, H.64, V.68, H.93 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

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

HEM.2: 20 residues within 4Å: Chain A: Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.1 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:Y.43, A:Y.43, A:F.44, A:F.44, A:V.63, A:A.66, A:L.67, A:L.84, A:L.87, A:L.92, A:V.94, A:F.99, A:F.99, A:V.133, A:L.137 Water bridges: A:H.59 Salt bridges: A:H.46, A:K.62 Metal complexes: A:H.88 HEM.5: 18 residues within 4Å: Chain B: T.39, F.42, F.43, H.64, K.67, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, V.138, L.142 Ligands: OXY.4 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:T.39, B:F.42, B:F.42, B:F.43, B:F.43, B:F.72, B:F.72, B:L.89, B:L.92, B:L.97, B:V.99, B:N.103, B:F.104, B:L.107, B:V.138, B:L.142 Water bridges: B:S.45, B:H.64 Salt bridges: B:H.64 Metal complexes: B:H.93 HEM.7: 18 residues within 4Å: Chain C: Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 Ligands: OXY.6 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.43, C:Y.43, C:Y.43, C:F.44, C:F.44, C:F.47, C:V.63, C:L.84, C:L.92, C:V.94, C:F.99, C:F.99, C:L.102, C:V.133, C:L.137 Water bridges: C:H.59 Salt bridges: C:K.62 Metal complexes: C:H.88 HEM.10: 18 residues within 4Å: Chain D: T.39, F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: OXY.9 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:T.39, D:F.42, D:F.42, D:F.43, D:F.43, D:V.68, D:A.71, D:F.72, D:F.72, D:L.89, D:L.97, D:V.99, D:N.103, D:F.104, D:L.107, D:L.142 Water bridges: D:S.45, D:S.45 Metal complexes: D:H.93

2 x MW0: (5-methylfuran-2-yl)methanol(Covalent)

MW0.3: 8 residues within 4Å: Chain A: V.2, L.3, K.128, A.131, S.132, T.135 Chain C: T.135, S.139 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.2, A:A.131 Hydrogen bonds: A:T.135 MW0.8: 7 residues within 4Å: Chain A: T.135, S.139 Chain C: V.2, L.3, A.131, S.132, T.135 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.2, C:L.3, C:A.131 Hydrogen bonds: C:T.135, C:T.135 Water bridges: C:T.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alhashimi, R.T. et al., Design, Synthesis, and Antisickling Investigation of a Nitric Oxide-Releasing Prodrug of 5HMF for the Treatment of Sickle Cell Disease. Biomolecules (2022)

Release Date

2022-03-30

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

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