Research workbench
Crystal structure of the gap domain of SMAP1L (LOC64744) stromal membrane-associated protein 1-like
Analyse Crystal structure of the gap domain of SMAP1L (LOC64744) stromal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IQJ
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromal membrane-associated protein 1-like
- UniProt
- Q8WU79
- Ligands
- ZN, UNX
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stromal membrane-associated protein 1-like | protein | 118 | 43% helix, 9% strand | Q8WU79 |
| B | Stromal membrane-associated protein 1-like | protein | 123 | 41% helix, 9% strand | Q8WU79 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.62 | 0.78 | 35 | BME |
| 2 | 119 | 0.41 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 2IQJ · Crystal structure of the GAP domain of SMAP1L (LOC64744) stromal membrane-associated… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WU79 · AlphaFold monomer V2.0 prediction for stromal membrane-associated protein 2 (Q8WU79) · a predicted model of the same protein · chain A 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 Q8WU79
- Elsewhere: RCSB PDB 2IQJ · PDBe 2IQJ · UniProt Q8WU79
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