MolNFT v1 · #111550 · protein
Crystal structure of mongoose (helogale parvula) hemoglobin at pH 7.0
4YU4: “Crystal structure of mongoose (helogale parvula) hemoglobin at pH 7.0”. X-ray diffraction, 2 ligands (HEM, OXY), 6 pockets (best druggability 0.78). MolNFT v1 #111550 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YU4
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin
- Ligands
- HEM, OXY
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin | protein | 141 | 77% helix, 0% strand | — |
| B, D | Hemoglobin | protein | 146 | 80% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.78 | 0.89 | 57 | empty |
| 2 | 258 | 0.75 | 0.88 | 29 | HEM, OXY |
| 3 | 262 | 0.73 | 0.86 | 30 | OXY, HEM |
| 4 | 224 | 0.73 | 0.87 | 29 | HEM, OXY |
| 5 | 240 | 0.72 | 0.86 | 30 | OXY, HEM |
Interfaces
6 interfaces between chains.
- A–B · 892 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 861 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 496 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4YU4 · Crystal structure of Mongoose (Helogale parvula) hemoglobin at pH 7.0 · 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
- Elsewhere: RCSB PDB 4YU4 · PDBe 4YU4
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