MolNFT v1 · #127023 · protein
Crystal structure of bacillus subtilis ywea
5MKD: “Crystal structure of bacillus subtilis ywea”. X-ray diffraction, 2 pockets (best druggability 0.69). MolNFT v1 #127023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MKD
- Type
- protein
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ywea
- UniProt
- A0A164UMC7
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ywea | protein | 124 | 6% helix, 48% strand | A0A164UMC7 |
| D | Ywea | protein | 122 | 5% helix, 48% strand | A0A164UMC7 |
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 | 978 | 0.69 | 0.74 | 67 | empty |
| 2 | 75 | 0.38 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 637 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 635 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 230 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MKD · Crystal structure of Bacillus subtilis Ywea · 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 A0A164UMC7
- Elsewhere: RCSB PDB 5MKD · PDBe 5MKD · UniProt A0A164UMC7
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