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SMTL ID : 5x2r.2 (2 other biounits)

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 10 mM phosphate pH 6.9.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x HNI: PROTOPORPHYRIN IX CONTAINING NI(II)(Non-covalent)

HNI.1:

18 residues within 4Å:

Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136

19 PLIP interactions:

19 interactions with chain A,

Hydrophobic interactions: A:Y.42, A:Y.42, A:V.62, A:V.62, A:L.83, A:L.86, A:L.91, A:L.91, A:V.93, A:N.97, A:F.98, A:F.98, A:L.101, A:V.132, A:L.136
Salt bridges: A:H.45, A:K.61
pi-Stacking: A:H.58, A:H.87

HNI.4:

18 residues within 4Å:

Chain D: T.38, F.41, F.42, 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, V.137, L.141

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:V.67, D:V.67, D:F.71, D:L.88, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:V.137
pi-Cation interactions: D:H.63
Metal complexes: D:H.92

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

HEM.2:

18 residues within 4Å:

Chain B: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, K.95, L.96, V.98, N.102, F.103, L.106, L.141

19 PLIP interactions:

19 interactions with chain B,

Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:V.67, B:V.67, B:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141
Salt bridges: B:K.66, B:K.95
Metal complexes: B:H.92

HEM.3:

19 residues within 4Å:

Chain C: M.32, T.39, Y.42, F.43, F.46, H.58, K.61, V.62, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, V.132, L.136

16 PLIP interactions:

16 interactions with chain C,

Hydrophobic interactions: C:Y.42, C:F.43, C:F.43, C:F.43, C:V.62, C:V.62, C:L.83, C:L.86, C:L.91, C:V.93, C:F.98, C:V.132, C:L.136
Salt bridges: C:K.61
pi-Stacking: C:H.58
Metal complexes: C:H.87

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shibayama, N. et al., Direct observation of conformational population shifts in crystalline human hemoglobin. J. Biol. Chem. (2017)

Release Date

2017-09-20

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

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Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Hemoglobin subunit alpha

Toggle Identical (AC)

Hemoglobin subunit beta

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