SMTL ID : 7ud7.1

Crystal structure of deoxygenated hemoglobin in complex with 5HMF-NO at 1.8 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 16 residues within 4Å: Chain A: Y.43, F.44, H.46, F.47, H.59, K.62, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:Y.43, A:F.44, A:F.44, A:F.44, A:F.47, A:K.62, A:K.62, A:A.66, A:L.84, A:L.84, A:L.87, A:L.92, A:V.94, A:V.94, A:F.99, A:L.102, A:L.137 Water bridges: A:K.62 Salt bridges: A:H.46, A:K.62, A:K.62 pi-Stacking: A:H.59 Metal complexes: A:H.88 HEM.3: 19 residues within 4Å: Chain B: L.32, F.42, F.43, H.64, K.67, V.68, A.71, F.72, F.86, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, V.138, L.142 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:L.32, B:F.42, B:F.42, B:F.43, B:F.43, B:K.67, B:V.68, B:F.72, B:F.86, B:L.89, B:L.89, B:L.92, B:L.97, B:V.99, B:F.104, B:L.107, B:V.138, B:L.142 Water bridges: B:K.67 Salt bridges: B:K.67 pi-Stacking: B:H.64 Metal complexes: B:H.93 HEM.4: 19 residues within 4Å: Chain C: M.33, T.40, Y.43, F.44, H.46, 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, L.137 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:Y.43, C:F.44, C:K.62, C:K.62, C:V.63, C:A.66, C:L.84, C:L.87, C:L.92, C:L.92, C:V.94, C:V.94, C:F.99, C:L.102, C:L.137 Water bridges: C:K.62 Salt bridges: C:H.46, C:K.62 pi-Stacking: C:H.59 Metal complexes: C:H.88 HEM.6: 17 residues within 4Å: Chain D: L.32, F.42, F.43, F.46, H.64, V.68, A.71, F.72, L.92, H.93, L.97, V.99, N.103, F.104, L.107, V.138, L.142 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:L.32, D:F.42, D:F.42, D:F.43, D:V.68, D:F.72, D:L.92, D:L.97, D:L.97, D:V.99, D:F.104, D:L.107, D:V.138, D:L.142 pi-Stacking: D:H.64 Metal complexes: D:H.93

2 x MWC: dihydroxy[(5-methylfuran-2-yl)methoxy]amine(Covalent)

MWC.2: 6 residues within 4Å: Chain A: V.2, L.3 Chain C: T.138, S.139, Y.141, R.142 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.138 Water bridges: C:R.142, C:R.142 Hydrophobic interactions: A:V.2 MWC.5: 7 residues within 4Å: Chain A: T.138, S.139, Y.141, R.142 Chain C: V.2, L.3 Chain D: W.38 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.2 Hydrogen bonds: A:T.138 Water bridges: A:R.142, A:R.142

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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