SMTL ID : 5x2s.3 (2 other biounits)

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 6.5.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-2-2-mer

Ligands

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

HNI.1: 20 residues within 4Å: Chain A: M.32, T.39, 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 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:F.46, A:K.61, A:K.61, A:V.62, A:A.65, A:L.83, A:L.91, A:V.93, A:V.93, A:F.98, A:F.98, A:V.132, A:L.136 Salt bridges: A:K.61, A:K.90 pi-Stacking: A:H.58, A:H.87 HNI.5: 16 residues within 4Å: Chain D: L.31, F.41, F.42, H.63, K.66, V.67, A.70, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:L.31, D:F.41, D:F.42, D:F.42, D:K.66, D:V.67, D:V.67, D:A.70, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 pi-Stacking: D:H.63 Metal complexes: D:H.92

1 x PEM: 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID(Non-covalent)

PEM.2: 9 residues within 4Å: Chain A: P.95, K.99, T.134, T.137, Y.140 Chain B: Y.35, W.37 Chain C: P.95, K.127 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:P.95, B:W.37, A:P.95, A:Y.140 Salt bridges: C:K.127

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

HEM.3: 18 residues within 4Å: Chain B: L.31, 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 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:L.31, B:F.41, B:F.41, B:F.42, B:F.42, B:F.42, B:K.66, B:V.67, B:V.67, B:A.70, B:F.71, B:L.88, B:L.91, B:L.96, B:L.96, B:V.98, B:V.98, B:F.103, B:F.103, B:L.141 Salt bridges: B:K.59, B:H.63 pi-Stacking: B:H.63 Metal complexes: B:H.92 HEM.4: 17 residues within 4Å: Chain C: 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, L.136 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.42, C:F.46, C:V.62, C:A.65, C:L.83, C:L.83, C:L.86, C:L.91, C:L.91, C:V.93, C:F.98, C:F.98, C:L.101, C:L.136 Salt bridges: C:H.45 pi-Stacking: C:H.58 pi-Cation interactions: 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

2017-09-27

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
K

B
J

D
L

Hemoglobin subunit alpha

Hemoglobin subunit beta

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