Research workbench
Crystal structure of SAV_2001 protein from streptomyces avermitilis, northeast structural genomics consortium target SVR107.
Analyse Crystal structure of SAV_2001 protein from streptomyces avermitilis, northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DEX
- Type
- protein
- Length
- 635 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAV_2001
- UniProt
- Q82LK9
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | SAV_2001 | protein | 79 | 35% helix, 34% strand | Q82LK9 |
| B | SAV_2001 | protein | 80 | 36% helix, 30% strand | Q82LK9 |
| C, G | SAV_2001 | protein | 77 | 35% helix, 35% strand | Q82LK9 |
| D | SAV_2001 | protein | 81 | 33% helix, 33% strand | Q82LK9 |
| H | SAV_2001 | protein | 83 | 35% helix, 33% strand | Q82LK9 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.70 | 0.97 | 16 | empty |
| 2 | 61 | 0.70 | 0.97 | 16 | empty |
| 3 | 164 | 0.64 | 0.86 | 30 | empty |
| 4 | 160 | 0.63 | 0.85 | 30 | empty |
| 5 | 243 | 0.61 | 0.81 | 32 | empty |
Interfaces
13 interfaces between chains.
- E–F · 893 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 877 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 864 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 442 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3DEX · Crystal structure of SAV_2001 protein from Streptomyces avermitilis, Northeast Structural… · 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 Q82LK9
- Elsewhere: RCSB PDB 3DEX · PDBe 3DEX · UniProt Q82LK9
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