Research workbench
Crystal structure of uncharacterized protein ymzc precursor from bacillus subtilis, northeast structural genomics consortium target SR378A
Analyse Crystal structure of uncharacterized protein ymzc precursor from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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