Research workbench
Crystal structure of deoxy hemoglobin in complex with beta CYS93 modifying agent, TD3
Analyse Crystal structure of deoxy hemoglobin in complex with beta CYS93 modifying… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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