Research workbench
The heme-bound structure of the chloroplast protein AT3G03890
Analyse The heme-bound structure of the chloroplast protein AT3G03890 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M0A
- Type
- protein
- Length
- 1,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AT3G03890 protein
- UniProt
- Q8LDU1
- Ligands
- HEM, AZI
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AT3G03890 protein | protein | 255 | 36% helix, 33% strand | Q8LDU1 |
| B, C | AT3G03890 protein | protein | 256 | 36% helix, 33% strand | Q8LDU1 |
| D | AT3G03890 protein | protein | 249 | 35% helix, 32% strand | Q8LDU1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- AZI · Azide ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.80 | 0.82 | 120 | HEM |
| 2 | 916 | 0.77 | 0.79 | 94 | empty |
| 3 | 438 | 0.73 | 0.83 | 47 | HEM, AZI |
| 4 | 417 | 0.72 | 0.83 | 48 | HEM |
| 5 | 401 | 0.71 | 0.82 | 43 | HEM |
Interfaces
3 interfaces between chains.
- C–D · 1507 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1484 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 221 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6M0A · The heme-bound structure of the chloroplast protein At3g03890 · 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 Q8LDU1
- Elsewhere: RCSB PDB 6M0A · PDBe 6M0A · UniProt Q8LDU1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.