SMTL ID : 4ni1.1

Quaternary R CO-liganded hemoglobin structure in complex with a thiol containing compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.1: 5 residues within 4Å: Chain A: L.29, H.58, V.62, H.87 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) CMO.7: 5 residues within 4Å: Chain B: L.28, H.63, V.67, H.92 Ligands: HEM.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 CMO.11: 5 residues within 4Å: Chain C: L.29, H.58, V.62, H.87 Ligands: HEM.12 No protein-ligand interaction detected (PLIP) CMO.17: 5 residues within 4Å: Chain D: L.28, H.63, V.67, H.92 Ligands: HEM.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.63

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

HEM.2: 19 residues within 4Å: Chain A: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.1 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:F.46, A:L.66, A:L.83, A:L.91, A:V.93, A:F.98, A:L.101, A:L.136 Water bridges: A:H.58 Salt bridges: A:H.45, A:K.61 Metal complexes: A:H.87 HEM.8: 17 residues within 4Å: Chain B: T.38, F.41, F.42, 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: CMO.7 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:A.70, B:F.71, B:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:F.103, B:L.106, B:L.141 Metal complexes: B:H.92 HEM.12: 19 residues within 4Å: Chain C: T.39, Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.11 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:Y.42, C:F.43, C:F.46, C:L.66, C:L.83, C:L.91, C:V.93, C:F.98, C:L.101, C:L.136 Water bridges: C:H.58 Salt bridges: C:H.45, C:K.61 Metal complexes: C:H.87 HEM.18: 17 residues within 4Å: Chain D: T.38, F.41, F.42, 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: CMO.17 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:A.70, D:F.71, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:F.103, D:L.106, D:L.141 Metal complexes: D:H.92

8 x 2JX: 5-[(2R)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione(Non-covalent)(Covalent)

2JX.3: 12 residues within 4Å: Chain A: K.99, S.102, H.103, L.106, D.126 Chain B: Y.35, W.37, E.101 Chain C: P.95 Ligands: 2JX.4, 2JX.10, 2JX.14 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.103, A:L.106 Hydrogen bonds: A:K.99, A:K.99, B:Y.35 2JX.4: 10 residues within 4Å: Chain A: P.95, F.98, K.99, A.130, S.133, T.137, R.141 Ligands: 2JX.3, 2JX.13, 2JX.14 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:K.99, A:A.130 Hydrogen bonds: A:T.137, A:R.141 pi-Cation interactions: A:K.99 Water bridges: C:K.99 2JX.9: 9 residues within 4Å: Chain B: C.93, V.98, P.100, F.103, A.142, K.144 Chain C: S.35, F.36 Chain D: A.135 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:A.142 Hydrophobic interactions: C:F.36, C:F.36, D:A.135 2JX.10: 11 residues within 4Å: Chain A: L.100, H.103, L.106, H.122 Chain B: Y.35, E.101, L.105, N.108, V.109, C.112 Ligands: 2JX.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.100 Hydrogen bonds: A:H.103, A:H.122, B:N.108 2JX.13: 12 residues within 4Å: Chain A: P.95 Chain C: K.99, S.102, H.103, L.106, D.126 Chain D: Y.35, W.37, E.101 Ligands: 2JX.4, 2JX.14, 2JX.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.103, C:L.106 Hydrogen bonds: C:K.99, C:K.99 2JX.14: 10 residues within 4Å: Chain C: P.95, F.98, K.99, A.130, S.133, T.137, R.141 Ligands: 2JX.3, 2JX.4, 2JX.13 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Water bridges: A:K.99 Hydrophobic interactions: C:K.99, C:A.130 Hydrogen bonds: C:T.137, C:T.137, C:R.141 pi-Cation interactions: C:K.99 2JX.19: 9 residues within 4Å: Chain A: S.35, F.36 Chain B: A.135 Chain D: C.93, V.98, P.100, F.103, A.142, K.144 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: D:A.142 Hydrophobic interactions: B:A.135, A:F.36, A:F.36 2JX.20: 11 residues within 4Å: Chain C: L.100, H.103, L.106, H.122 Chain D: Y.35, E.101, L.105, N.108, V.109, C.112 Ligands: 2JX.13 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.35, D:N.108, C:H.103, C:H.122 Hydrophobic interactions: C:L.100

4 x MBN: TOLUENE(Non-covalent)

MBN.5: 7 residues within 4Å: Chain A: A.21, Y.24, G.25, L.66, L.105, L.109 Ligands: MBN.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.24, A:L.66, A:L.105, A:L.109, A:L.109, A:L.109 MBN.6: 7 residues within 4Å: Chain A: A.13, W.14, V.17, T.67, V.70, L.109 Ligands: MBN.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.13, A:V.17, A:V.70, A:L.109 MBN.15: 7 residues within 4Å: Chain C: A.21, Y.24, G.25, L.66, L.105, L.109 Ligands: MBN.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.24, C:L.66, C:L.105, C:L.109, C:L.109, C:L.109 MBN.16: 7 residues within 4Å: Chain C: A.13, W.14, V.17, T.67, V.70, L.109 Ligands: MBN.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.13, C:V.17, C:V.70, C:L.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakagawa, A. et al., Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling. Acs Chem.Biol. (2014)

Release Date

2014-09-17

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin subunit alpha

Hemoglobin subunit beta

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