MolNFT v1 · #49096 · protein
Nbla protein from T. vulcanus
2QDO: “Nbla protein from T. vulcanus”. X-ray diffraction, 3 pockets (best druggability 0.71). MolNFT v1 #49096 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QDO
- Type
- protein
- Length
- 211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nbla protein
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nbla protein | protein | 53 | 83% helix, 0% strand | — |
| B, D | Nbla protein | protein | 52 | 79% helix, 0% strand | — |
| C | Nbla protein | protein | 54 | 81% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.71 | 0.75 | 70 | empty |
| 2 | 66 | 0.33 | 0.76 | 16 | empty |
| 3 | 52 | 0.28 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1695 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1644 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 198 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2QDO · NblA protein from T. vulcanus · 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
- Elsewhere: RCSB PDB 2QDO · PDBe 2QDO
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