Research workbench
Direct observation of conformational population shifts in hemoglobin: crystal structure of half-liganded hemoglobin after adding 4 mm bezafibrate pH 7.2.
Analyse Direct observation of conformational population shifts in hemoglobin: crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X2T
- Type
- protein
- Length
- 1,710 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HNI, HEM, PEM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemoglobin subunit alpha | protein | 140 | 75% helix, 0% strand | P69905 |
| B, D, F, H, J, L | Hemoglobin subunit beta | protein | 145 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- HNI · Protoporphyrin IX containing ni(ii) · ligand · 6 copies · chains A, D, E, H, I, L
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains B, C, F, G, J, K
- PEM · 2-[P-[2-P-chlorobenzamido)ethyl]phenoxy]-2-methylpropionic acid · ligand · chains I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.86 | 0.87 | 92 | empty |
| 2 | 934 | 0.85 | 0.86 | 100 | empty |
| 3 | 750 | 0.83 | 0.86 | 85 | PEM |
| 4 | 1012 | 0.75 | 0.78 | 78 | empty |
| 5 | 238 | 0.74 | 0.88 | 29 | HEM |
Interfaces
24 interfaces between chains.
- I–J · 945 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 885 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 880 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5X2T · Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 5X2T · PDBe 5X2T · UniProt P69905 · UniProt P68871
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