MolNFT v1 · #69615 · protein
Crystal structure of uncharacterized protein ymzc precursor from bacillus subtilis, northeast structural genomics consortium target SR378A
3KVP: “Crystal structure of uncharacterized protein ymzc precursor from bacillus subtilis, northeast structural…”. X-ray diffraction, 2 pockets (best druggability 0.71). MolNFT v1 #69615 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KVP
- Type
- protein
- Length
- 265 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein ymzc
- UniProt
- O31797
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein ymzc | protein | 43 | 0% helix, 63% strand | O31797 |
| C | Uncharacterized protein ymzc | protein | 45 | 11% helix, 62% strand | O31797 |
| D | Uncharacterized protein ymzc | protein | 49 | 16% helix, 55% strand | O31797 |
| E | Uncharacterized protein ymzc | protein | 43 | 7% helix, 63% strand | O31797 |
| F | Uncharacterized protein ymzc | protein | 42 | 0% helix, 55% strand | O31797 |
Ligands and binding sites
- ACY · Acetic acid · additive · 2 copies · chains B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.71 | 0.81 | 65 | ACY |
| 2 | 64 | 0.38 | 0.79 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1003 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 892 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 862 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 847 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 830 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3KVP · Crystal Structure of Uncharacterized protein ymzC Precursor from Bacillus subtilis… · the same entry in another collection · chain F against F, TM-score 1.00
- O31797 · AlphaFold monomer V2.0 prediction for uncharacterized protein ymzc (O31797) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O31797
- Elsewhere: RCSB PDB 3KVP · PDBe 3KVP · UniProt O31797
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