SMTL ID : 1shr.1

Crystal structure of ferrocyanide bound human hemoglobin A2 at 1.88A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-2-2-mer

Ligands

10 x CYN: CYANIDE ION(Non-covalent)(Non-functional Binders)

CYN.1: 5 residues within 4Å: Chain A: L.29, F.43, H.58, V.62 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CYN.4: 5 residues within 4Å: Chain B: L.28, F.42, H.63, V.67 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) CYN.6: 7 residues within 4Å: Chain B: K.82, H.143 Ligands: CYN.7, CYN.13, CYN.14, CYN.15, CYN.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.82 CYN.7: 9 residues within 4Å: Chain B: H.143, H.146 Chain D: K.82, H.146 Ligands: FE.5, CYN.6, CYN.13, CYN.15, CYN.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.82 CYN.9: 5 residues within 4Å: Chain C: L.29, F.43, H.58, V.62 Ligands: HEM.10 No protein-ligand interaction detected (PLIP) CYN.11: 5 residues within 4Å: Chain D: L.28, F.42, H.63, V.67 Ligands: HEM.17 No protein-ligand interaction detected (PLIP) CYN.13: 5 residues within 4Å: Chain D: K.82 Ligands: CYN.6, CYN.7, CYN.14, CYN.16 No protein-ligand interaction detected (PLIP) CYN.14: 4 residues within 4Å: Ligands: CYN.6, CYN.13, CYN.15, CYN.16 No protein-ligand interaction detected (PLIP) CYN.15: 6 residues within 4Å: Chain D: Y.145, H.146 Ligands: CYN.6, CYN.7, CYN.14, CYN.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.146, D:H.146 CYN.16: 9 residues within 4Å: Chain D: K.82, H.143, Y.145 Ligands: CYN.6, CYN.7, FE.12, CYN.13, CYN.14, CYN.15 No protein-ligand interaction detected (PLIP)

3 x FE: FE (III) ION(Non-covalent)

FE.2: 3 residues within 4Å: Chain A: D.75, M.76, P.77 No protein-ligand interaction detected (PLIP) FE.5: 4 residues within 4Å: Chain B: H.143, H.146 Chain D: H.146 Ligands: CYN.7 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Metal complexes: D:H.146, B:H.143, B:H.146 FE.12: 3 residues within 4Å: Chain D: H.143, Y.145 Ligands: CYN.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.143

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

HEM.3: 16 residues within 4Å: Chain A: 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: CYN.1 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:F.46, A:A.65, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:F.98, A:L.101, A:L.136 Water bridges: A:K.61, A:K.61, A:K.61, A:K.61 Salt bridges: A:K.61 pi-Stacking: A:H.58, A:H.87, A:H.87 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: CYN.4 23 PLIP interactions: 23 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:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:L.106, B:L.141 Water bridges: B:H.63, B:H.63, B:K.66, B:K.66 Salt bridges: B:H.63, B:K.66 pi-Stacking: B:H.63, B:H.92, B:H.92 Metal complexes: B:H.92 HEM.10: 18 residues within 4Å: Chain C: 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: CYN.9 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:F.46, 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:K.61, C:K.61 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58, C:H.87, C:H.87 Metal complexes: C:H.87 HEM.17: 19 residues within 4Å: Chain D: T.38, F.41, F.42, F.45, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CYN.11 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Water bridges: D:S.44, D:K.59, D:H.63 Salt bridges: D:H.63 pi-Stacking: D:H.63, D:H.92, D:H.92 Metal complexes: D:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sen, U. et al., Crystal structures of HbA2 and HbE and modeling of hemoglobin delta4: interpretation of the thermal stability and the antisickling effect of HbA2 and identification of the ferrocyanide binding site in Hb. Biochemistry (2004)

Release Date

2004-10-26

Peptides

Hemoglobin alpha chain: AC
Hemoglobin delta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin alpha chain

Hemoglobin delta chain

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