MolNFT v1 · #70494 · protein
Crystal structure of stage V sporulation protein ad (spovad) from bacillus subtilis, northeast structural genomics consortium target SR525
3LM6: “Crystal structure of stage V sporulation protein ad (spovad) from bacillus subtilis, northeast structural…”. X-ray diffraction, 4 pockets (best druggability 0.81). MolNFT v1 #70494 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LM6
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stage V sporulation protein ad
- UniProt
- P40869
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stage V sporulation protein ad | protein | 334 | 40% helix, 25% strand | P40869 |
| B | Stage V sporulation protein ad | protein | 322 | 40% helix, 26% strand | P40869 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.81 | 0.89 | 44 | empty |
| 2 | 456 | 0.68 | 0.79 | 51 | empty |
| 3 | 102 | 0.44 | 0.78 | 15 | empty |
| 4 | 103 | 0.41 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2499 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3LM6 · Crystal Structure of Stage V sporulation protein AD (spoVAD) from Bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- P40869 · AlphaFold monomer V2.0 prediction for stage V sporulation protein ad (P40869) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P40869
- Elsewhere: RCSB PDB 3LM6 · PDBe 3LM6 · UniProt P40869
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