Research workbench
Crystal structure of AL2 pal domain in complex with ATRING1A distal site
Analyse Crystal structure of AL2 pal domain in complex with ATRING1A distal site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVW
- Type
- protein
- Length
- 548 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein alfin-like 2; ATRING1A distal binding site
- UniProt
- Q9SRM4, F4K8U4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein alfin-like 2 | protein | 132 | 56% helix, 8% strand | Q9SRM4 |
| B, C, E | Phd finger protein alfin-like 2 | protein | 131 | 57% helix, 6% strand | Q9SRM4 |
| D | ATRING1A distal binding site | protein | 12 | 0% helix, 17% strand | F4K8U4 |
| F | ATRING1A distal binding site | protein | 11 | 0% helix, 18% strand | F4K8U4 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.74 | 0.88 | 42 | empty |
| 2 | 897 | 0.73 | 0.77 | 71 | empty |
| 3 | 64 | 0.73 | 0.98 | 18 | empty |
| 4 | 65 | 0.72 | 0.97 | 16 | empty |
| 5 | 209 | 0.72 | 0.88 | 41 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1504 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1503 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 582 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 413 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5XVW · Crystal structure of AL2 PAL domain in complex with AtRing1a distal site · the same entry in another collection · chain F against F, TM-score 1.00
- Q9SRM4 · AlphaFold monomer V2.0 prediction for phd finger protein alfin-like 2 (Q9SRM4) · a predicted model of the same protein · chain E 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 Q9SRM4
- Every structure of UniProt F4K8U4
- Elsewhere: RCSB PDB 5XVW · PDBe 5XVW · UniProt Q9SRM4 · UniProt F4K8U4
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