MolNFT v1 · #46164 · protein
X-ray crystal structure of protein ytmb from bacillus subtilis. northeast structural genomics consortium target SR466
2NWA · Hypothetical protein ytmb: “X-ray crystal structure of protein ytmb from bacillus subtilis. northeast structural genomics consortium…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.76). MolNFT v1 #46164 on…
- PDB
- 2NWA
- Type
- protein
- Length
- 640 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ytmb
- UniProt
- O34365
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Hypothetical protein ytmb | protein | 80 | 0% helix, 56% strand | O34365 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.76 | 0.80 | 82 | SO4 |
| 2 | 304 | 0.59 | 0.77 | 43 | SO4 |
| 3 | 210 | 0.58 | 0.80 | 38 | empty |
| 4 | 159 | 0.56 | 0.81 | 33 | empty |
| 5 | 124 | 0.43 | 0.76 | 21 | empty |
Interfaces
16 interfaces between chains.
- C–D · 841 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 824 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 800 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 775 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 477 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2NWA · X-ray Crystal Structure of Protein ytmB from Bacillus subtilis. Northeast Structural… · the same entry in another collection · chain H against H, TM-score 1.00
- O34365 · AlphaFold monomer V2.0 prediction for uncharacterized protein ytmb (O34365) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O34365
- Elsewhere: RCSB PDB 2NWA · PDBe 2NWA · UniProt O34365
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