MolNFT v1 · #116977 · protein
Crystal structure of E. COLI ybgjk
5DUD · Ybgk: “Crystal structure of E. COLI ybgjk”. X-ray diffraction, 19 pockets (best druggability 0.77). MolNFT v1 #116977 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DUD
- Type
- protein
- Length
- 992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ybgk; Ybgj
- UniProt
- P75745, P0AAV4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ybgk | protein | 300 | 17% helix, 28% strand | P75745 |
| B | Ybgj | protein | 200 | 27% helix, 32% strand | P0AAV4 |
| C | Ybgk | protein | 295 | 17% helix, 27% strand | P75745 |
| D | Ybgj | protein | 197 | 22% helix, 32% strand | P0AAV4 |
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.77 | 0.79 | 89 | empty |
| 2 | 324 | 0.74 | 0.86 | 36 | empty |
| 3 | 414 | 0.74 | 0.84 | 45 | empty |
| 4 | 89 | 0.72 | 0.95 | 25 | empty |
| 5 | 149 | 0.50 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1563 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1552 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 181 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DUD · Crystal structure of E. coli YbgJK · the same entry in another collection · chain D against D, TM-score 1.00
- P75745 · AlphaFold monomer V2.0 prediction for 5-oxoprolinase subunit C (P75745) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0AAV4 · AlphaFold monomer V2.0 prediction for 5-oxoprolinase subunit B (P0AAV4) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P75745
- Every structure of UniProt P0AAV4
- Elsewhere: RCSB PDB 5DUD · PDBe 5DUD · UniProt P75745 · UniProt P0AAV4
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