Research workbench
SARM1 SAM1-2 domains
Analyse SARM1 SAM1-2 domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QWV
- Type
- protein
- Length
- 2,337 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterile alpha and tir motif-containing protein 1
- UniProt
- Q6SZW1
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 11 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Sterile alpha and tir motif-containing protein 1 | protein | 143 | 64% helix, 0% strand | Q6SZW1 |
| B | Sterile alpha and tir motif-containing protein 1 | protein | 157 | 62% helix, 0% strand | Q6SZW1 |
| C, K | Sterile alpha and tir motif-containing protein 1 | protein | 148 | 64% helix, 0% strand | Q6SZW1 |
| D | Sterile alpha and tir motif-containing protein 1 | protein | 146 | 65% helix, 0% strand | Q6SZW1 |
| E | Sterile alpha and tir motif-containing protein 1 | protein | 146 | 65% helix, 0% strand | Q6SZW1 |
| F, P | Sterile alpha and tir motif-containing protein 1 | protein | 144 | 65% helix, 0% strand | Q6SZW1 |
| G, L | Sterile alpha and tir motif-containing protein 1 | protein | 145 | 63% helix, 0% strand | Q6SZW1 |
| H | Sterile alpha and tir motif-containing protein 1 | protein | 146 | 64% helix, 0% strand | Q6SZW1 |
| I | Sterile alpha and tir motif-containing protein 1 | protein | 145 | 64% helix, 0% strand | Q6SZW1 |
| J | Sterile alpha and tir motif-containing protein 1 | protein | 147 | 65% helix, 0% strand | Q6SZW1 |
| M, O | Sterile alpha and tir motif-containing protein 1 | protein | 145 | 63% helix, 0% strand | Q6SZW1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, B, C, D, E, F, I, J, K, L, M, N, H, O, P
- BME · Beta-mercaptoethanol · additive · 16 copies · chains A, H, B, C, D, E, F, G, I, J, K, L, M, N, O, P
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, C, D, I, J, K
- PGE · Triethylene glycol · additive · 2 copies · chains B, I, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.77 | 0.83 | 100 | BME, EDO |
| 2 | 309 | 0.68 | 0.83 | 45 | empty |
| 3 | 220 | 0.63 | 0.82 | 34 | EDO, PEG, BME |
| 4 | 207 | 0.62 | 0.83 | 30 | empty |
| 5 | 198 | 0.62 | 0.83 | 40 | empty |
Interfaces
17 interfaces between chains.
- K–L · 874 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 863 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 860 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 850 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6QWV · SARM1 SAM1-2 domains · the same entry in another collection · chain K against K, 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 Q6SZW1
- Elsewhere: RCSB PDB 6QWV · PDBe 6QWV · UniProt Q6SZW1
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