SMTL ID : 3wtg.1

Crystal structure of Emu (dromaius novaehollandiae) hemoglobin at 2.3 angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: 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, V.133, L.137 Ligands: OXY.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:Y.43, A:Y.43, A:F.44, A:F.44, A:F.47, A:K.62, A:V.63, A:A.66, A:L.67, A:L.84, A:L.92, A:V.94, A:N.98, A:F.99, A:F.99, A:L.102, A:L.102, A:V.133, A:L.137 Water bridges: A:K.62 Salt bridges: A:K.62 pi-Stacking: A:H.59, A:H.59 Metal complexes: A:H.88 HEM.3: 19 residues within 4Å: Chain B: L.31, T.38, F.41, F.42, H.63, K.66, S.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, V.137, L.141 Ligands: OXY.4 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:L.31, B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.71, B:L.88, B:L.96, B:V.98, B:N.102, B:F.103, B:F.103, B:V.137, B:L.141 Salt bridges: B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.5: 17 residues within 4Å: Chain C: Y.43, F.44, H.46, F.47, H.59, K.62, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 Ligands: OXY.6 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:Y.43, C:F.44, C:L.84, C:L.92, C:V.94, C:F.99, C:F.99, C:L.102, C:L.137 Salt bridges: C:H.46, C:K.62 pi-Stacking: C:H.59 Metal complexes: C:H.88 HEM.7: 20 residues within 4Å: Chain D: L.31, T.38, F.41, F.42, F.45, H.63, K.66, S.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: OXY.8 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:L.31, D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:F.71, D:F.71, D:F.85, D:L.88, D:L.91, D:L.96, D:V.98, D:F.103, D:F.103, D:L.141 Hydrogen bonds: D:S.44 Water bridges: D:H.63, D:H.63 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 4 residues within 4Å: Chain A: H.59, V.63, H.88 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.59 OXY.4: 5 residues within 4Å: Chain B: F.42, H.63, V.67, H.92 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) OXY.6: 5 residues within 4Å: Chain C: F.44, H.59, V.63, H.88 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.59 OXY.8: 4 residues within 4Å: Chain D: H.63, V.67, H.92 Ligands: HEM.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abubakkar, M.M. et al., Purification and preliminary structural studies of hemoglobin from high oxygen affinity species Emu (Dromaius novaehollandiae) at neutral pH. To be Published

Release Date

2014-07-02

Peptides

Hemoglobin subunit alpha-A: AC
Hemoglobin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha-A

Hemoglobin