Research workbench
Crystal structure of the SDF2-like protein from arabidopsis thaliana
Analyse Crystal structure of the SDF2-like protein from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MAL
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromal cell-derived factor 2-like protein
- UniProt
- Q93ZE8
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Stromal cell-derived factor 2-like protein | protein | 181 | 5% helix, 46% strand | Q93ZE8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 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 | 370 | 0.66 | 0.80 | 42 | empty |
| 2 | 50 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 877 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3MAL · Crystal structure of the SDF2-like protein from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q93ZE8 · AlphaFold monomer V2.0 prediction for stromal cell-derived factor 2-like protein (Q93ZE8) · 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 Q93ZE8
- Elsewhere: RCSB PDB 3MAL · PDBe 3MAL · UniProt Q93ZE8
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