MolNFT v1 · #51500 · protein
Crystal structure of yage, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. COLI K12
2V9D: “Crystal structure of yage, a prophage protein belonging to the dihydrodipicolinic acid synthase family from…”. X-ray diffraction, 7 pockets (best druggability 0.69). MolNFT v1 #51500 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2V9D
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yage
- UniProt
- P75682
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Yage | protein | 298 | 51% helix, 12% strand | P75682 |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.69 | 0.89 | 35 | empty |
| 2 | 166 | 0.68 | 0.88 | 34 | empty |
| 3 | 245 | 0.62 | 0.81 | 40 | empty |
| 4 | 266 | 0.62 | 0.80 | 35 | empty |
| 5 | 271 | 0.62 | 0.80 | 35 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1702 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1698 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1031 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1031 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2V9D · Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid… · the same entry in another collection · chain A against A, TM-score 1.00
- P75682 · AlphaFold monomer V2.0 prediction for putative 2-dehydro-3-deoxy-D- gluconate aldolase… · a predicted model of the same protein · 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 P75682
- Elsewhere: RCSB PDB 2V9D · PDBe 2V9D · UniProt P75682
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