MolNFT v1 · #100454 · protein
Crystal structure of GCN5-related N-acetyltransferase from kribbella flavida
4MY3: “Crystal structure of GCN5-related N-acetyltransferase from kribbella flavida”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.89). MolNFT v1 #100454 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MY3
- Type
- protein
- Length
- 2,320 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GCN5-related N-acetyltransferase
- UniProt
- D2PVF8
- Ligands
- CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | GCN5-related N-acetyltransferase | protein | 386 | 37% helix, 32% strand | D2PVF8 |
| B | GCN5-related N-acetyltransferase | protein | 392 | 35% helix, 31% strand | D2PVF8 |
| D | GCN5-related N-acetyltransferase | protein | 384 | 35% helix, 33% strand | D2PVF8 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.89 | 0.90 | 131 | empty |
| 2 | 1192 | 0.88 | 0.89 | 144 | EDO |
| 3 | 1198 | 0.87 | 0.89 | 131 | empty |
| 4 | 987 | 0.81 | 0.82 | 121 | empty |
| 5 | 1156 | 0.77 | 0.79 | 102 | CL |
Interfaces
12 interfaces between chains.
- C–D · 2154 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2121 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2043 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 752 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 744 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 4MY3 · Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida · the same entry in another collection · chain D against D, 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 D2PVF8
- Elsewhere: RCSB PDB 4MY3 · PDBe 4MY3 · UniProt D2PVF8
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