MolNFT v1 · #38139 · protein
Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40W
2GNW · Non-symbiotic hemoglobin 1: “Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40W”. X-ray diffraction, 1 ligand (HEM), 6 pockets (best druggability 0.74). MolNFT v1 #38139 on GenesisL1: 3D structure…
- PDB
- 2GNW
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-symbiotic hemoglobin 1
- UniProt
- O04986
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-symbiotic hemoglobin 1 | protein | 165 | 66% helix, 0% strand | O04986 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.74 | 0.86 | 33 | HEM |
| 2 | 241 | 0.72 | 0.86 | 29 | HEM |
| 3 | 283 | 0.57 | 0.77 | 33 | empty |
| 4 | 50 | 0.53 | 0.88 | 14 | empty |
| 5 | 192 | 0.47 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2GNW · Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40W · the same entry in another collection · chain A against A, TM-score 1.00
- O04986 · AlphaFold monomer V2.0 prediction for non-symbiotic hemoglobin 1 (O04986) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 O04986
- Elsewhere: RCSB PDB 2GNW · PDBe 2GNW · UniProt O04986
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