Research workbench
Rational modification of vanillin derivatives to stereospecifically destabilize sickle hemoglobin polymer formation
Analyse Rational modification of vanillin derivatives to stereospecifically destabilize… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DI4
- 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, GJ1, CMO
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 75% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- GJ1 · {6-[(4-methoxy-2-methylphenoxy)methyl]pyridin-2-yl}methanol · ligand · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.80 | 0.90 | 52 | empty |
| 2 | 226 | 0.74 | 0.88 | 28 | CMO, HEM |
| 3 | 201 | 0.73 | 0.88 | 26 | CMO, HEM |
| 4 | 199 | 0.71 | 0.87 | 24 | CMO, HEM |
| 5 | 186 | 0.69 | 0.86 | 24 | CMO, HEM |
Interfaces
6 interfaces between chains.
- C–D · 908 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 899 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6DI4 · Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle… · 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 6DI4 · PDBe 6DI4 · UniProt P69905 · UniProt P68871
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