SMTL ID : 5e29.1

Crystal Structure of Deoxygenated Hemoglobin in Complex with an Allosteric Effector and Nitric Oxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NO: NITRIC OXIDE(Non-covalent)

NO.1: 4 residues within 4Å: Chain A: L.29, H.58, V.62 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) NO.8: 4 residues within 4Å: Chain C: L.29, H.58, V.62 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

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

HEM.2: 20 residues within 4Å: Chain A: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: NO.1 21 PLIP interactions: 20 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.46, A:V.62, A:A.65, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:F.98, A:L.101, A:L.136 Water bridges: A:H.58, A:K.61 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.58 Metal complexes: NO.1 HEM.5: 17 residues within 4Å: Chain B: L.30, F.40, F.41, F.44, H.62, K.65, V.66, A.69, L.87, L.90, H.91, L.95, V.97, N.101, F.102, L.105, L.140 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.30, B:F.40, B:F.40, B:F.41, B:F.41, B:K.65, B:V.66, B:V.66, B:L.87, B:L.90, B:L.95, B:L.95, B:V.97, B:N.101, B:F.102, B:L.105, B:L.140 Salt bridges: B:H.62, B:K.65 pi-Stacking: B:H.62 Metal complexes: B:H.91 HEM.9: 18 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, F.46, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: NO.8 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:F.43, C:L.83, C:L.83, C:L.86, C:L.91, C:L.91, C:V.93, C:F.98, C:F.98, C:L.136 Water bridges: C:K.61, C:K.61, C:K.61 Salt bridges: C:K.61 pi-Stacking: C:H.58, C:H.58, C:H.87, C:H.87 Metal complexes: NO.8 HEM.10: 17 residues within 4Å: Chain D: L.30, F.40, F.41, F.44, H.62, K.65, V.66, A.69, L.87, L.90, H.91, L.95, V.97, N.101, F.102, L.105, L.140 24 PLIP interactions: 24 interactions with chain D, Hydrophobic interactions: D:F.40, D:F.40, D:F.41, D:F.41, D:F.41, D:K.65, D:K.65, D:V.66, D:L.87, D:L.90, D:L.95, D:V.97, D:V.97, D:N.101, D:F.102, D:L.105, D:L.105, D:L.140 Water bridges: D:H.62, D:H.62, D:K.65 Salt bridges: D:H.62 pi-Stacking: D:H.62 Metal complexes: D:H.91

1 x 5JN: 2-(nitrooxy)ethyl 2-(4-{2-[(3,5-dimethylphenyl)amino]-2-oxoethyl}phenoxy)-2-methylpropanoate(Non-covalent)

5JN.3: 14 residues within 4Å: Chain A: K.99, L.100, H.103, A.130, S.131, T.134 Chain B: Y.34, W.36, N.107 Chain C: P.95, T.137, Y.140, R.141 Ligands: RQ3.6 11 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: C:Y.140, B:Y.34, B:W.36, A:K.99, A:H.103 Water bridges: C:T.137, B:N.107, B:N.107, A:T.134 Salt bridges: C:R.141 pi-Cation interactions: A:K.99

2 x RQ3: 2-{4-[(3,5-DIMETHYLANILINO)-CARBONYL-METHYL]-PHENOXY}-2-METHYLPROPIONIC ACID(Non-covalent)

RQ3.4: 10 residues within 4Å: Chain A: P.95, T.137, R.141 Chain C: F.36, K.99, L.100, H.103 Chain D: Y.34, W.36, N.107 16 PLIP interactions: 6 interactions with chain D, 4 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: D:Y.34, D:W.36, D:W.36, A:P.95, A:R.141, C:F.36, C:K.99, C:L.100, C:H.103 Water bridges: D:Y.34, D:N.107, D:N.107, A:R.141, A:R.141 Salt bridges: C:K.99 pi-Cation interactions: C:K.99 RQ3.6: 12 residues within 4Å: Chain A: F.36, K.99, L.100, H.103 Chain B: Y.34, W.36, N.107 Chain C: P.95, T.137, Y.140, R.141 Ligands: 5JN.3 16 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: C:P.95, C:Y.140, C:R.141, B:Y.34, B:W.36, B:W.36, A:F.36, A:K.99, A:H.103 Water bridges: C:T.137, C:R.141, B:N.107, B:N.107, A:K.99, A:K.99 pi-Cation interactions: A:K.99

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 4 residues within 4Å: Chain B: K.94, H.96 Chain C: P.44, H.45 2 PLIP interactions: 2 interactions with chain C Water bridges: C:P.44, C:H.45 NO3.12: 3 residues within 4Å: Chain D: D.93, K.94, H.96 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.93 Water bridges: D:K.94

1 x CAC: CACODYLATE ION(Non-functional Binders)

CAC.11: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:K.81, D:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, G.G. et al., Design, Synthesis, and Investigation of Novel Nitric Oxide (NO)-Releasing Prodrugs as Drug Candidates for the Treatment of Ischemic Disorders: Insights into NO-Releasing Prodrug Biotransformation and Hemoglobin-NO Biochemistry. Biochemistry (2015)

Release Date

2015-10-14

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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