MolNFT v1 · #182677 · protein
Structure of yeby from E. COLI K12
7N0J: “Structure of yeby from E. COLI K12”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #182677 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7N0J
- Type
- protein
- Length
- 1,112 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeby
- UniProt
- P64506
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yeby | protein | 94 | 27% helix, 26% strand | P64506 |
| C | Yeby | protein | 91 | 26% helix, 26% strand | P64506 |
| D, G, K | Yeby | protein | 93 | 27% helix, 31% strand | P64506 |
| E | Yeby | protein | 95 | 25% helix, 33% strand | P64506 |
| F, B, L | Yeby | protein | 92 | 25% helix, 26% strand | P64506 |
| H, J | Yeby | protein | 92 | 25% helix, 26% strand | P64506 |
| I | Yeby | protein | 93 | 28% helix, 28% strand | P64506 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.76 | 0.80 | 76 | empty |
| 2 | 443 | 0.62 | 0.76 | 44 | empty |
| 3 | 339 | 0.61 | 0.78 | 43 | empty |
| 4 | 188 | 0.46 | 0.75 | 38 | empty |
| 5 | 110 | 0.42 | 0.77 | 26 | empty |
Interfaces
10 interfaces between chains.
- D–G · 576 Ų buried · 4 hydrogen bonds · protein-protein
- K–L · 554 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 549 Ų buried · 1 hydrogen bond · protein-protein
- A–J · 539 Ų buried · 6 hydrogen bonds · protein-protein
- F–I · 532 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 12 disulfide (engineered, disulfide).
Compared structures
- 7N0J · Structure of YebY from E. coli K12 · the same entry in another collection · chain L against L, 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 P64506
- Elsewhere: RCSB PDB 7N0J · PDBe 7N0J · UniProt P64506
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