MolNFT v1 · #140261 · protein
Crystal structure of AL2 pal domain in complex with ATBMI1B binding site
5Y53 · Phd finger protein alfin-like 2: “Crystal structure of AL2 pal domain in complex with ATBMI1B binding site”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #140261 on GenesisL1: 3D structure, binding sites and…
- 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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