MolNFT v1 · #67888 · protein
RING1B C-terminal DOMAIN/RYBP C-terminal domain complex
3IXS · E3 ubiquitin-protein ligase RING2: “RING1B C-terminal DOMAIN/RYBP C-terminal domain complex”. X-ray diffraction, 18 pockets (best druggability 0.64). MolNFT v1 #67888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IXS
- Type
- protein
- Length
- 812 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RING2; RING1 and YY1-binding protein
- EC
- 6.3.2.-
- UniProt
- Q99496, Q8N488
- Pockets
- 18 · best druggability 0.64
Structure
x-ray diffraction · 10 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 111 | 28% helix, 28% strand | Q99496 |
| B | RING1 and YY1-binding protein | protein | 31 | 0% helix, 74% strand | Q8N488 |
| D | RING1 and YY1-binding protein | protein | 34 | 0% helix, 68% strand | Q8N488 |
| E | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 101 | 28% helix, 31% strand | Q99496 |
| F, L | RING1 and YY1-binding protein | protein | 32 | 9% helix, 53% strand | Q8N488 |
| G | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 99 | 28% helix, 33% strand | Q99496 |
| H | RING1 and YY1-binding protein | protein | 36 | 0% helix, 64% strand | Q8N488 |
| I | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 95 | 27% helix, 34% strand | Q99496 |
| J | RING1 and YY1-binding protein | protein | 30 | 0% helix, 77% strand | Q8N488 |
| K | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 100 | 22% helix, 32% strand | Q99496 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, D, E, G, H
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.64 | 0.76 | 64 | empty |
| 2 | 280 | 0.61 | 0.80 | 32 | empty |
| 3 | 83 | 0.56 | 0.86 | 19 | NHE |
| 4 | 307 | 0.55 | 0.76 | 32 | empty |
| 5 | 155 | 0.43 | 0.75 | 20 | empty |
Interfaces
25 interfaces between chains.
- C–D · 1077 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1068 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1032 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 988 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 959 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3IXS · Ring1B C-terminal domain/RYBP C-terminal domain Complex · the same entry in another collection · chain L against L, TM-score 1.00
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 Q99496
- Every structure of UniProt Q8N488
- Elsewhere: RCSB PDB 3IXS · PDBe 3IXS · UniProt Q99496 · UniProt Q8N488
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.