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
- 6ZG1
- Type
- protein
- Length
- 1,175 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterile alpha and tir motif-containing protein 1
- EC
- 3.2.2.6, 3.2.2.-
- UniProt
- Q6SZW1
- Pockets
- 12 · best druggability 0.71
Structure
electron microscopy · 8 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 143 | 64% helix, 0% strand | Q6SZW1 |
| B | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 157 | 62% helix, 0% strand | Q6SZW1 |
| C | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 148 | 64% helix, 0% strand | Q6SZW1 |
| D | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 146 | 65% helix, 0% strand | Q6SZW1 |
| E | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 146 | 65% helix, 0% strand | Q6SZW1 |
| F | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 144 | 65% helix, 0% strand | Q6SZW1 |
| G | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 145 | 63% helix, 0% strand | Q6SZW1 |
| H | Sterile alpha and tir motif-containing protein 1 (EC 3.2.2.6, 3.2.2.-) | protein | 146 | 64% helix, 0% strand | Q6SZW1 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, E, F
- BME · Beta-mercaptoethanol · additive · 8 copies · chains A, H, B, C, D, E, F, G
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.71 | 0.82 | 51 | EDO, PEG |
| 2 | 352 | 0.70 | 0.83 | 54 | empty |
| 3 | 177 | 0.61 | 0.83 | 27 | empty |
| 4 | 134 | 0.58 | 0.84 | 23 | empty |
| 5 | 77 | 0.57 | 0.87 | 21 | PGE |
Interfaces
8 interfaces between chains.
- C–D · 864 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 860 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 851 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 846 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6ZG1 · SARM1 SAM1-2 domains · 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 Q6SZW1
- Elsewhere: RCSB PDB 6ZG1 · PDBe 6ZG1 · UniProt Q6SZW1
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