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Crystal structure of the stage V sporulation protein ad (spovad) from bacillus licheniformis. northeast structural genomics consortium target BIR6.
Analyse Crystal structure of the stage V sporulation protein ad (spovad) from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMA
- Type
- protein
- Length
- 1,258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stage V sporulation protein ad (spovad)
- UniProt
- Q65HU8
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stage V sporulation protein ad (spovad) | protein | 309 | 38% helix, 25% strand | Q65HU8 |
| B | Stage V sporulation protein ad (spovad) | protein | 311 | 39% helix, 24% strand | Q65HU8 |
| C | Stage V sporulation protein ad (spovad) | protein | 327 | 37% helix, 23% strand | Q65HU8 |
| D | Stage V sporulation protein ad (spovad) | protein | 311 | 40% helix, 24% strand | Q65HU8 |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.78 | 0.81 | 106 | empty |
| 2 | 77 | 0.61 | 0.90 | 19 | empty |
| 3 | 155 | 0.52 | 0.79 | 31 | empty |
| 4 | 138 | 0.50 | 0.79 | 21 | empty |
| 5 | 67 | 0.49 | 0.84 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2426 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2270 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 482 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3LMA · Crystal structure of the stage V sporulation protein AD (SpoVAD) from Bacillus… · 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 Q65HU8
- Elsewhere: RCSB PDB 3LMA · PDBe 3LMA · UniProt Q65HU8
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