MolNFT v1 · #59800 · protein
Crystal structure of putative acetyltransferase (YP_390128.1) from desulfovibrio desulfuricans G20 at 2.28 a resolution
3C8V: “Crystal structure of putative acetyltransferase (YP_390128.1) from desulfovibrio desulfuricans G20 at 2.28 a…”. X-ray diffraction, 2 ligands (MG, CL), 16 pockets (best druggability 0.78). MolNFT v1 #59800 on GenesisL1: 3D structure…
- PDB
- 3C8V
- Type
- protein
- Length
- 1,843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acetyltransferase
- UniProt
- Q30V63
- Ligands
- MG, CL
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative acetyltransferase | protein | 453 | 17% helix, 38% strand | Q30V63 |
| B | Putative acetyltransferase | protein | 461 | 15% helix, 36% strand | Q30V63 |
| C | Putative acetyltransferase | protein | 465 | 16% helix, 35% strand | Q30V63 |
| D | Putative acetyltransferase | protein | 464 | 16% helix, 37% strand | Q30V63 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · 12 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.78 | 0.80 | 109 | empty |
| 2 | 898 | 0.75 | 0.79 | 93 | CL, EDO |
| 3 | 635 | 0.72 | 0.80 | 73 | EDO |
| 4 | 691 | 0.72 | 0.79 | 69 | EDO |
| 5 | 602 | 0.72 | 0.79 | 69 | MG |
Interfaces
6 interfaces between chains.
- A–D · 1393 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1271 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1231 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3C8V · Crystal structure of putative acetyltransferase (YP_390128.1) from Desulfovibrio… · the same entry in another collection · 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 Q30V63
- Elsewhere: RCSB PDB 3C8V · PDBe 3C8V · UniProt Q30V63
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