Research workbench
Crystal structure of the putative acetyltransferase of gnat family from shigella flexneri
Analyse Crystal structure of the putative acetyltransferase of gnat family from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PDO
- Type
- protein
- Length
- 1,122 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyltransferase ypea
- EC
- 2.3.1.-
- UniProt
- P63422
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acetyltransferase ypea (EC 2.3.1.-) | protein | 140 | 36% helix, 34% strand | P63422 |
| B | Acetyltransferase ypea (EC 2.3.1.-) | protein | 141 | 36% helix, 31% strand | P63422 |
| D | Acetyltransferase ypea (EC 2.3.1.-) | protein | 142 | 37% helix, 31% strand | P63422 |
| E, H | Acetyltransferase ypea (EC 2.3.1.-) | protein | 140 | 34% helix, 31% strand | P63422 |
| F | Acetyltransferase ypea (EC 2.3.1.-) | protein | 141 | 36% helix, 32% strand | P63422 |
| G | Acetyltransferase ypea (EC 2.3.1.-) | protein | 138 | 37% helix, 33% strand | P63422 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains B, H, D, E, G
- EDO · 1,2-ethanediol · additive · 7 copies · chains D, E, F, A, B, G, H
- ACY · Acetic acid · additive · 2 copies · chains A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.80 | 0.87 | 59 | empty |
| 2 | 507 | 0.80 | 0.86 | 58 | empty |
| 3 | 238 | 0.75 | 0.89 | 38 | EDO |
| 4 | 96 | 0.68 | 0.92 | 21 | empty |
| 5 | 55 | 0.54 | 0.89 | 13 | empty |
Interfaces
21 interfaces between chains.
- A–B · 2499 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 2492 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2487 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2439 Ų buried · 45 hydrogen bonds · protein-protein
- F–H · 555 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 2PDO · Crystal Structure of the Putative Acetyltransferase of GNAT Family from Shigella flexneri · the same entry in another collection · chain H against H, TM-score 1.00
- P63422 · AlphaFold monomer V2.0 prediction for acetyltransferase ypea (P63422) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P63422
- Elsewhere: RCSB PDB 2PDO · PDBe 2PDO · UniProt P63422
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