SMTL ID : 1yvt.1

The high salt (phosphate) crystal structure of CO Hemoglobin E (Glu26Lys) at physiological pH (pH 7.35)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: T.39, Y.42, F.43, H.45, 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.2 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:F.43, A:K.61, A:L.66, A:L.83, A:L.83, A:L.86, A:L.91, A:V.93, A:V.93, A:F.98, A:L.101, A:L.136 Water bridges: A:K.61, A:K.61 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.87, A:H.87 Metal complexes: A:H.87, CMO.2 HEM.3: 18 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, V.137, L.141 Ligands: CMO.4 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.71, B:F.71, B:L.88, B:L.91, B:L.91, B:L.96, B:V.98, B:N.102, B:L.106, B:V.137, B:L.141 pi-Stacking: B:H.63, B:H.92, B:H.92 Metal complexes: B:H.92, CMO.4 HEM.6: 18 residues within 4Å: Chain C: T.39, Y.42, F.43, H.45, 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.7 24 PLIP interactions: 23 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:K.61, C:L.66, C:L.83, C:L.83, C:L.86, C:L.91, C:V.93, C:V.93, 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, CMO.7 HEM.8: 18 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, V.137, L.141 Ligands: CMO.9 20 PLIP interactions: 19 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.71, D:F.71, D:L.88, D:L.91, D:L.91, D:L.96, D:V.98, D:N.102, D:L.106, D:V.137, D:L.141 pi-Stacking: D:H.63, D:H.92, D:H.92 Metal complexes: D:H.92, CMO.9

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

CMO.2: 6 residues within 4Å: Chain A: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CMO.4: 4 residues within 4Å: Chain B: H.63, V.67, H.92 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.7: 6 residues within 4Å: Chain C: L.29, F.43, H.58, V.62, H.87 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 CMO.9: 4 residues within 4Å: Chain D: H.63, V.67, H.92 Ligands: HEM.8 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: V.96, K.99 Chain B: E.101, R.104 Chain C: K.99 Chain D: E.101 Ligands: GOL.10 7 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:E.101, A:K.99, B:R.104 Water bridges: D:E.101, A:K.99, C:K.99, C:K.99 GOL.10: 7 residues within 4Å: Chain A: K.99 Chain B: E.101 Chain C: V.96, K.99 Chain D: E.101, R.104 Ligands: GOL.5 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B, 2 interactions with chain C Water bridges: A:K.99, A:K.99, B:E.101, C:K.99 Hydrogen bonds: D:R.104, C:K.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.N. et al., The high salt (phosphate) crystal structure of CO Hemoglobin E (Glu26Lys) at physiological pH (pH 7.35). To be Published

Release Date

2006-02-28

Peptides

Hemoglobin alpha chain: AC
Hemoglobin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Hemoglobin alpha chain

Hemoglobin beta chain

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