Research workbench
Direct observation of conformational population shifts in hemoglobin: crystal structure of half-liganded hemoglobin after adding 80 mm phosphate pH 6.7.
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
- 5X2U
- 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
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemoglobin subunit alpha | protein | 140 | 76% helix, 0% strand | P69905 |
| B, D, F, H, J, L | Hemoglobin subunit beta | protein | 145 | 79% 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
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 | 1036 | 0.86 | 0.87 | 91 | empty |
| 2 | 1070 | 0.86 | 0.87 | 97 | empty |
| 3 | 1104 | 0.83 | 0.84 | 95 | empty |
| 4 | 99 | 0.76 | 0.96 | 18 | empty |
| 5 | 247 | 0.75 | 0.88 | 30 | HEM |
Interfaces
25 interfaces between chains.
- K–L · 958 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 942 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 926 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 919 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5X2U · 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 5X2U · PDBe 5X2U · UniProt P69905 · UniProt P68871
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