Research workbench
Crystal structure of T-state human hemoglobin complexed with three L35 molecules
Analyse Crystal structure of T-state human hemoglobin complexed with three L35 molecules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5Z
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha subunit; Hemoglobin beta subunit
- UniProt
- P69905, P68871
- Ligands
- HEM, L35
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha subunit | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D | Hemoglobin beta subunit | protein | 145 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- L35 · 2-[4-({[(3,5-dichlorophenyl)amino]carbonyl}amino)phenoxy]-2-methylpropanoic acid · ligand · 3 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.82 | 0.84 | 70 | L35 |
| 2 | 213 | 0.75 | 0.90 | 29 | HEM |
| 3 | 251 | 0.74 | 0.87 | 32 | HEM |
| 4 | 221 | 0.73 | 0.88 | 30 | HEM |
| 5 | 227 | 0.71 | 0.86 | 29 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 846 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 839 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 721 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 718 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2D5Z · Crystal structure of T-state human hemoglobin complexed with three L35 molecules · 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 2D5Z · PDBe 2D5Z · UniProt P69905 · UniProt P68871
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