Research workbench
Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40L
Analyse Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GNV
- Type
- protein
- Length
- 313 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
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-symbiotic hemoglobin 1 | protein | 158 | 73% helix, 0% strand | O04986 |
| B | Non-symbiotic hemoglobin 1 | protein | 155 | 71% helix, 0% strand | O04986 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.75 | 0.87 | 31 | HEM, DIO |
| 2 | 240 | 0.74 | 0.88 | 30 | HEM, DIO |
| 3 | 87 | 0.35 | 0.74 | 18 | empty |
| 4 | 54 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 518 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2GNV · Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40L · 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 0.93
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 2GNV · PDBe 2GNV · UniProt O04986
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