MolNFT v1 · #171351 · protein
Crystal structure of type-I ribosome-inactivating protein trichobakin (tbk)
6Z1Y: “Crystal structure of type-I ribosome-inactivating protein trichobakin (tbk)”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.82). MolNFT v1 #171351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z1Y
- Type
- protein
- Length
- 981 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trichobakin
- UniProt
- Q9LRE3
- Ligands
- NA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trichobakin | protein | 244 | 41% helix, 25% strand | Q9LRE3 |
| B | Trichobakin | protein | 243 | 40% helix, 26% strand | Q9LRE3 |
| C | Trichobakin | protein | 248 | 38% helix, 25% strand | Q9LRE3 |
| D | Trichobakin | protein | 246 | 38% helix, 25% strand | Q9LRE3 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.82 | 0.84 | 96 | empty |
| 2 | 908 | 0.79 | 0.82 | 92 | NA |
| 3 | 379 | 0.57 | 0.75 | 51 | empty |
| 4 | 168 | 0.51 | 0.79 | 22 | empty |
| 5 | 92 | 0.45 | 0.80 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 682 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 650 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6Z1Y · Crystal structure of type-I ribosome-inactivating protein trichobakin (TBK) · 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 Q9LRE3
- Elsewhere: RCSB PDB 6Z1Y · PDBe 6Z1Y · UniProt Q9LRE3
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