Research workbench
Crystal structure of the protein ATU1372 with unknown function from agrobacterium tumefaciens
Analyse Crystal structure of the protein ATU1372 with unknown function from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D01
- Type
- protein
- Length
- 1,888 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A9CJ63
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 41% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 158 | 42% helix, 30% strand | A9CJ63 |
| B | Uncharacterized protein | protein | 157 | 40% helix, 32% strand | A9CJ63 |
| C, H, J | Uncharacterized protein | protein | 157 | 41% helix, 32% strand | A9CJ63 |
| D | Uncharacterized protein | protein | 156 | 42% helix, 31% strand | A9CJ63 |
| E | Uncharacterized protein | protein | 155 | 41% helix, 33% strand | A9CJ63 |
| F | Uncharacterized protein | protein | 158 | 41% helix, 32% strand | A9CJ63 |
| G | Uncharacterized protein | protein | 157 | 41% helix, 31% strand | A9CJ63 |
| I | Uncharacterized protein | protein | 159 | 42% helix, 32% strand | A9CJ63 |
| K | Uncharacterized protein | protein | 157 | 41% helix, 32% strand | A9CJ63 |
| L | Uncharacterized protein | protein | 160 | 41% helix, 32% strand | A9CJ63 |
Ligands and binding sites
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 12 copies · chains A, I, L, B, C, H, J, E, G, K, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.87 | 0.95 | 46 | empty |
| 2 | 416 | 0.87 | 0.95 | 43 | empty |
| 3 | 93 | 0.79 | 0.99 | 28 | empty |
| 4 | 86 | 0.77 | 0.99 | 21 | empty |
| 5 | 80 | 0.77 | 0.99 | 20 | empty |
Interfaces
24 interfaces between chains.
- C–F · 1106 Ų buried · 21 hydrogen bonds · protein-protein
- D–H · 1098 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 1095 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 1094 Ų buried · 20 hydrogen bonds · protein-protein
- E–L · 1092 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3D01 · Crystal structure of the protein Atu1372 with unknown function from Agrobacterium… · the same entry in another collection · chain D against D, 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 A9CJ63
- Elsewhere: RCSB PDB 3D01 · PDBe 3D01 · UniProt A9CJ63
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