MolNFT v1 · #144539 · protein
Crystal structure of deoxy hemoglobin in complex with beta CYS93 modifying agent, TD3
6BWP · Hemoglobin subunit alpha: “Crystal structure of deoxy hemoglobin in complex with beta CYS93 modifying agent, TD3”. X-ray diffraction, 2 ligands (HEM, EBJ), 11 pockets (best druggability 0.79). MolNFT v1 #144539 on GenesisL1: 3D…
- PDB
- 6BWP
- Type
- protein
- Length
- 574 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, EBJ
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 79% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- EBJ · 1H-1,2,3-triazole-5-thiol · 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 | 661 | 0.79 | 0.84 | 65 | empty |
| 2 | 245 | 0.74 | 0.87 | 28 | HEM |
| 3 | 212 | 0.73 | 0.88 | 30 | HEM |
| 4 | 214 | 0.73 | 0.88 | 30 | HEM |
| 5 | 251 | 0.69 | 0.84 | 28 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 852 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 838 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 730 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 720 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6BWP · Crystal structure of Deoxy Hemoglobin in complex with beta Cys93 modifying agent, TD3 · 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 6BWP · PDBe 6BWP · UniProt P69905 · UniProt P68871
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