SMTL ID : 7uf6.1

Crystal structure of liganded Hb with the 5-HMF analog, MMA509

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: Y.43, F.44, H.46, F.47, H.59, K.62, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 Ligands: CMO.2 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:Y.43, A:Y.43, A:F.44, A:F.44, A:F.47, A:A.66, A:L.67, A:L.84, A:L.92, A:V.94, A:F.99, A:F.99, A:L.137 Salt bridges: A:H.46, A:K.62 Metal complexes: A:H.88 HEM.4: 19 residues within 4Å: Chain B: T.39, F.42, F.43, F.46, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: CMO.5 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:T.39, B:F.42, B:F.42, B:F.43, B:F.43, B:V.68, B:F.72, B:L.89, B:L.92, B:L.97, B:V.99, B:N.103, B:F.104, B:F.104, B:L.107, B:L.142 Water bridges: B:H.64, B:H.64, B:K.67, B:K.67 Salt bridges: B:H.64, B:K.67 Metal complexes: B:H.93 HEM.6: 18 residues within 4Å: Chain C: Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 Ligands: CMO.7 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:Y.43, C:Y.43, C:F.44, C:F.44, C:F.47, C:K.62, C:V.63, C:A.66, C:L.84, C:L.92, C:V.94, C:F.99, C:F.99, C:L.137 Water bridges: C:K.62, C:K.62, C:K.62 Salt bridges: C:K.62 Metal complexes: C:H.88 HEM.9: 18 residues within 4Å: Chain D: T.39, F.42, F.43, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Ligands: CMO.10 16 PLIP interactions: 16 interactions with chain D, Hydrophobic interactions: D:T.39, D:F.42, D:F.42, D:F.43, D:F.43, D:V.68, D:A.71, D:L.89, D:L.97, D:V.99, D:F.104, D:L.107, D:L.142 Water bridges: D:S.45 Salt bridges: D:H.64 Metal complexes: D:H.93

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

CMO.2: 6 residues within 4Å: Chain A: L.30, F.44, H.59, V.63, H.88 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CMO.5: 6 residues within 4Å: Chain B: L.29, F.43, H.64, V.68, H.93 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.7: 6 residues within 4Å: Chain C: L.30, F.44, H.59, V.63, H.88 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.59 CMO.10: 6 residues within 4Å: Chain D: L.29, F.43, H.64, V.68, H.93 Ligands: HEM.9 No protein-ligand interaction detected (PLIP)

2 x N1X: (2S)-2-(5-methylfuran-2-yl)oxane(Covalent)

N1X.3: 8 residues within 4Å: Chain A: V.2, L.3, P.78, S.132, V.136 Chain C: V.2, T.135, S.139 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.2, C:T.135, A:V.2, A:P.78, A:V.136 N1X.8: 7 residues within 4Å: Chain A: V.2, T.135 Chain C: V.2, M.77, P.78, S.132, V.136 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.2, C:P.78, C:V.136, A:V.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El-Araby, M.E. et al., Improving the antisickling activity of furaldehyde. To be published

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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