SMTL ID : 3ic0.1

Crystal Structure of liganded hemoglobin in complex with a potent antisickling agent, INN-298

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.29, F.43, H.58, V.62 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 OXY.5: 6 residues within 4Å: Chain B: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 OXY.7: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 OXY.12: 6 residues within 4Å: Chain D: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.13 No protein-ligand interaction detected (PLIP)

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

HEM.2: 20 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136 Ligands: OXY.1 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:K.61, A:V.62, A:A.65, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:L.101, A:V.132, A:L.136 Water bridges: A:H.58 Salt bridges: A:H.45 Metal complexes: A:H.87 HEM.6: 18 residues within 4Å: Chain B: T.38, F.41, F.42, F.45, H.63, K.66, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: OXY.5 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.71, B:F.71, B:L.88, B:L.96, B:V.98, B:F.103, B:L.106, B:L.141 Water bridges: B:H.63, B:K.66 Salt bridges: B:H.63, B:K.66 Metal complexes: B:H.92 HEM.8: 17 residues within 4Å: Chain C: Y.42, F.43, 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: OXY.7 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.46, C:K.61, C:A.65, C:L.83, C:L.91, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136 Water bridges: C:H.58, C:K.61 Salt bridges: C:K.61 Metal complexes: C:H.87 HEM.13: 18 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: OXY.12 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:L.88, D:L.96, D:V.98, D:N.102, D:F.103, D:F.103, D:L.106, D:L.141 Water bridges: D:S.44 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

4 x B77: 2-[(2-methoxy-5-methylphenoxy)methyl]pyridine(Covalent)(Non-covalent)

B77.3: 13 residues within 4Å: Chain A: V.1, L.2, D.126, K.127, A.130, S.131, T.134 Chain B: V.34, Y.35, W.37 Chain C: T.134, S.138 Ligands: B77.4 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:T.134, A:V.1, A:K.127, B:Y.35 B77.4: 12 residues within 4Å: Chain A: P.95, F.98, K.99, S.102, D.126, L.129, A.130, S.133 Chain B: W.37, E.101, L.105 Ligands: B77.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.98, A:K.99, A:K.99, A:L.129, A:A.130, B:L.105 Water bridges: A:K.99 B77.9: 13 residues within 4Å: Chain A: T.134, S.138 Chain C: V.1, L.2, D.126, K.127, A.130, S.131, T.134 Chain D: V.34, Y.35, W.37 Ligands: B77.10 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: C:V.1, C:L.2, C:K.127, A:T.134, D:Y.35 B77.10: 10 residues within 4Å: Chain C: P.95, F.98, K.99, S.102, D.126, A.130, S.133 Chain D: W.37, L.105 Ligands: B77.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.98, C:K.99, C:K.99, C:A.130, D:L.105

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 3 residues within 4Å: Chain C: D.85, H.89, K.90 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:H.89, C:K.90, C:K.139 SO4.14: 6 residues within 4Å: Chain D: V.1, L.78, D.79, N.80, L.81, K.82 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.79, D:L.81, D:K.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osheiza, A. et al., Structural and in Vitro Chracterization of Pridyl Derivatives of Benzaldehydes: Highly Potent Antisickling Agents. To be Published

Release Date

2009-07-28

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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