SMTL ID : 4l7y.1

Deoxygenated Hb in complex with the allosteric effectors, IRL2500 and 2,3-DPG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-mer

Ligands

4 x MH0: Mesoheme(Non-covalent)

MH0.1: 17 residues within 4Å: Chain A: M.32, Y.42, F.43, H.45, 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.46, A:A.65, A:L.83, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:V.93, A:F.98, A:L.136 Salt bridges: A:H.45, A:K.61, A:K.61 pi-Stacking: A:H.58, A:H.58 Metal complexes: A:H.87 MH0.2: 18 residues within 4Å: Chain B: L.31, F.41, F.42, F.45, H.63, K.66, V.67, A.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.141 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:L.31, B:F.41, B:F.41, B:F.42, B:K.66, B:V.67, B:F.71, B:F.85, B:L.88, B:L.91, B:L.96, B:L.96, B:V.98, B:N.102, B:F.103, B:L.141 Salt bridges: B:H.63 Metal complexes: B:H.92 MH0.4: 18 residues within 4Å: Chain C: M.32, 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 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.43, C:V.62, C:L.83, C:L.86, C:L.91, C:V.93, C:V.93, C:N.97, C:F.98, C:L.101, C:L.101, C:L.136 Water bridges: C:H.58 Salt bridges: C:H.45 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87 MH0.5: 16 residues within 4Å: Chain D: L.31, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, N.102, F.103, L.106, L.141 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:F.41, D:F.41, D:F.42, D:F.42, D:F.42, D:K.66, D:K.66, D:V.67, D:F.71, D:L.88, D:L.91, D:L.96, D:L.96, D:N.102, D:F.103, D:L.141 Water bridges: D:S.44 Salt bridges: D:H.63, D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

1 x IRL: (2R)-2-({(2S)-3-(biphenyl-4-yl)-2-[(3,5-dimethylbenzoyl)(methyl)amino]propanoyl}amino)-3-(1H-indol-3-yl)propanoic acid (non-preferred name)(Non-covalent)

IRL.3: 9 residues within 4Å: Chain B: K.82, N.139, H.143 Chain D: H.2, K.82, K.132, N.139 Ligands: DG2.6, DG2.7 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:H.2 Hydrogen bonds: D:N.139 Water bridges: D:K.82, D:K.82, D:N.139 Salt bridges: D:K.82 pi-Stacking: B:H.143 pi-Cation interactions: B:K.82

2 x DG2: (2R)-2,3-diphosphoglyceric acid(Non-covalent)

DG2.6: 6 residues within 4Å: Chain B: K.82, N.139 Chain D: K.82, H.143 Ligands: IRL.3, DG2.7 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain B Water bridges: D:K.82, B:K.82, B:K.82, B:K.82, B:K.82 Salt bridges: D:K.82, D:K.82, D:H.143, B:K.82 DG2.7: 4 residues within 4Å: Chain B: K.82 Chain D: K.82 Ligands: IRL.3, DG2.6 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B Salt bridges: D:K.82, D:K.82, B:K.82 Water bridges: B:K.82, B:K.82, B:K.82, B:K.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safo, M.K. et al., Novel small molecule modulators of human hemoglobin oxygen binding identified by small molecule microarray screening. To be Published

Release Date

2013-07-03

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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