Research workbench
Deoxyhemoglobin sh-drug complex
Analyse Deoxyhemoglobin sh-drug complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WCP
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, DG2
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 78% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 145 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- DG2 · (2R)-2,3-diphosphoglyceric acid · ligand · 2 copies · chains B, D
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 | 778 | 0.80 | 0.83 | 71 | empty |
| 2 | 240 | 0.73 | 0.87 | 29 | HEM |
| 3 | 205 | 0.72 | 0.88 | 31 | HEM |
| 4 | 209 | 0.72 | 0.87 | 31 | HEM |
| 5 | 254 | 0.70 | 0.85 | 32 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 856 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 837 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 723 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 718 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3WCP · Deoxyhemoglobin SH-drug complex · 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 3WCP · PDBe 3WCP · UniProt P69905 · UniProt P68871
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