Research workbench
Deoxygenated structure of a distal site hemoglobin mutant plus xe
Analyse Deoxygenated structure of a distal site hemoglobin mutant plus xe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W72
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human hemoglobin a
- UniProt
- P69905, P68871
- Ligands
- HEM, K, XE, SO4, PO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human hemoglobin a | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D | Human hemoglobin a | protein | 146 | 75% helix, 0% strand | P68871 |
| C | Human hemoglobin a | protein | 141 | 77% helix, 0% strand | P69905 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 3 copies · chains D, B, C
- XE · Xenon · ion · 15 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.79 | 0.84 | 68 | K, SO4, PO4 |
| 2 | 249 | 0.76 | 0.89 | 35 | HEM, XE |
| 3 | 184 | 0.70 | 0.87 | 27 | HEM, XE |
| 4 | 242 | 0.70 | 0.85 | 36 | HEM, XE |
| 5 | 190 | 0.70 | 0.87 | 31 | HEM, XE |
Interfaces
5 interfaces between chains.
- C–D · 853 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 841 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 718 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 712 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 363 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2W72 · Deoxygenated structure of a distal site hemoglobin mutant plus xe · 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 2W72 · PDBe 2W72 · UniProt P69905 · UniProt P68871
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