Research workbench
Human CtBP2(31-364) in complex with RAI2 peptide(315-322)
Analyse Human CtBP2(31-364) in complex with RAI2 peptide(315-322) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8ATI
- Type
- protein
- Length
- 1,331 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens
- Molecule
- Isoform 2 of C-terminal-binding protein 2; Retinoic acid-induced protein 2
- UniProt
- Q9Y5P3
- Ligands
- NAD
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Isoform 2 of C-terminal-binding protein 2 | protein | 330 | 36% helix, 16% strand | — |
| D | Isoform 2 of C-terminal-binding protein 2 | protein | 320 | 36% helix, 15% strand | — |
| a, b, c | Retinoic acid-induced protein 2 | protein | 7 | 0% helix, 29% strand | Q9Y5P3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.80 | 0.87 | 72 | NAD |
| 2 | 268 | 0.76 | 0.89 | 36 | NAD |
| 3 | 290 | 0.76 | 0.89 | 42 | NAD |
| 4 | 341 | 0.74 | 0.86 | 48 | NAD |
| 5 | 349 | 0.73 | 0.85 | 43 | empty |
Interfaces
7 interfaces between chains.
- C–D · 3287 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 20 hydrogen bonds · protein-protein
- B–b · 461 Ų buried · 3 hydrogen bonds · protein-protein
- C–c · 446 Ų buried · 4 hydrogen bonds · protein-protein
- A–a · 441 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- Q9Y5P3 · AlphaFold monomer V2.0 prediction for retinoic acid-induced protein 2 (Q9Y5P3) · a predicted model of the same protein · chain a against A, TM-score 0.35
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 Q9Y5P3
- Elsewhere: RCSB PDB 8ATI · PDBe 8ATI · UniProt Q9Y5P3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.