Research workbench
Crystal structure of protein DIP2308 from corynebacterium diphtheriae, northeast structural genomics consortium target CDR78
Analyse Crystal structure of protein DIP2308 from corynebacterium diphtheriae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PG5
- Type
- protein
- Length
- 1,213 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q6NEG6
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 298 | 50% helix, 12% strand | Q6NEG6 |
| B | Uncharacterized protein | protein | 301 | 51% helix, 12% strand | Q6NEG6 |
| C | Uncharacterized protein | protein | 312 | 49% helix, 12% strand | Q6NEG6 |
| D | Uncharacterized protein | protein | 302 | 48% helix, 12% strand | Q6NEG6 |
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 | 1072 | 0.88 | 0.89 | 146 | empty |
| 2 | 1073 | 0.87 | 0.89 | 133 | empty |
| 3 | 52 | 0.69 | 0.98 | 25 | empty |
| 4 | 64 | 0.55 | 0.88 | 15 | empty |
| 5 | 128 | 0.52 | 0.81 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1560 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1475 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1113 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1028 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 482 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3PG5 · Crystal structure of protein DIP2308 from Corynebacterium diphtheriae, Northeast… · 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 Q6NEG6
- Elsewhere: RCSB PDB 3PG5 · PDBe 3PG5 · UniProt Q6NEG6
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