Research workbench
Crystal structure of AL2 pal domain in complex with ATBMI1B binding site
Analyse Crystal structure of AL2 pal domain in complex with ATBMI1B binding site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y53
- Type
- protein
- Length
- 540 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein alfin-like 2; ATBMI1B binding site
- EC
- 2.3.2.27
- UniProt
- Q9SRM4, Q9M9Y4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein alfin-like 2 | protein | 132 | 58% helix, 8% strand | Q9SRM4 |
| B, C, E | Phd finger protein alfin-like 2 | protein | 131 | 55% helix, 6% strand | Q9SRM4 |
| D | ATBMI1B binding site (EC 2.3.2.27) | protein | 8 | 0% helix, 25% strand | Q9M9Y4 |
| F | ATBMI1B binding site (EC 2.3.2.27) | protein | 7 | 0% helix, 29% strand | Q9M9Y4 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.74 | 0.89 | 38 | empty |
| 2 | 253 | 0.74 | 0.88 | 38 | empty |
| 3 | 63 | 0.72 | 0.98 | 17 | empty |
| 4 | 63 | 0.72 | 0.98 | 19 | empty |
| 5 | 1174 | 0.72 | 0.75 | 76 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1471 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 1462 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 348 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 345 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 340 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5Y53 · Crystal structure of AL2 PAL domain in complex with AtBMI1b binding 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 1.00
- Q9M9Y4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin protein ligase DRIP1 (Q9M9Y4) · a predicted model of the same protein · chain F against A, TM-score 0.49
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 Q9M9Y4
- Elsewhere: RCSB PDB 5Y53 · PDBe 5Y53 · UniProt Q9SRM4 · UniProt Q9M9Y4
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