Research workbench
Crystal structure of a functionally unknown conserved protein from corynebacterium diphtheriae.
Analyse Crystal structure of a functionally unknown conserved protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDQ
- Type
- protein
- Length
- 609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized conserved protein
- UniProt
- Q6NFB0
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Uncharacterized conserved protein | protein | 152 | 67% helix, 9% strand | Q6NFB0 |
| C | Uncharacterized conserved protein | protein | 153 | 69% helix, 8% strand | Q6NFB0 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.64 | 0.75 | 82 | empty |
| 2 | 259 | 0.63 | 0.81 | 36 | empty |
| 3 | 113 | 0.60 | 0.86 | 21 | empty |
| 4 | 107 | 0.51 | 0.82 | 24 | empty |
| 5 | 174 | 0.48 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2371 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2326 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1791 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 343 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 327 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3KDQ · Crystal structure of a functionally unknown conserved protein from Corynebacterium… · 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 Q6NFB0
- Elsewhere: RCSB PDB 3KDQ · PDBe 3KDQ · UniProt Q6NFB0
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