Research workbench
Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a ring-E3- E2~UBIQUITIN-like protein-substrate intermediate trapped in action
Analyse Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a ring-E3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P5O
- Type
- protein
- Length
- 1,684 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-1; E3 ubiquitin-protein ligase RBX1; DCN1-like protein 1; NEDD8-conjugating enzyme…
- EC
- 6.3.2.-
- UniProt
- Q13616, P62877, Q96GG9, P61081, Q15843
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin-1 | protein | 327 | 56% helix, 13% strand | Q13616 |
| B | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 75 | 19% helix, 24% strand | P62877 |
| E | DCN1-like protein 1 | protein | 197 | 50% helix, 4% strand | Q96GG9 |
| I | NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) | protein | 169 | 31% helix, 17% strand | P61081 |
| K, H | NEDD8 | protein | 76 | 14% helix, 32% strand | Q15843 |
| C | Cullin-1 | protein | 322 | 55% helix, 10% strand | Q13616 |
| D | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 76 | 18% helix, 26% strand | P62877 |
| F | DCN1-like protein 1 | protein | 195 | 49% helix, 5% strand | Q96GG9 |
| G | NEDD8-conjugating enzyme UBC12 (EC 6.3.2.-) | protein | 171 | 31% helix, 17% strand | P61081 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.79 | 0.81 | 88 | empty |
| 2 | 1042 | 0.78 | 0.80 | 93 | empty |
| 3 | 764 | 0.75 | 0.80 | 69 | empty |
| 4 | 530 | 0.71 | 0.80 | 56 | empty |
| 5 | 390 | 0.65 | 0.78 | 45 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1588 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1578 Ų buried · 24 hydrogen bonds · protein-protein
- I–K · 882 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 869 Ų buried · 15 hydrogen bonds · protein-protein
- B–I · 707 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4P5O · Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like… · the same entry in another collection · chain D against D, TM-score 1.00
- Q96GG9 · AlphaFold monomer V2.0 prediction for DCN1-like protein 1 (Q96GG9) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 Q13616
- Every structure of UniProt P62877
- Every structure of UniProt Q96GG9
- Every structure of UniProt P61081
- Every structure of UniProt Q15843
- Elsewhere: RCSB PDB 4P5O · PDBe 4P5O · UniProt Q13616 · UniProt P62877 · UniProt Q96GG9 · UniProt P61081 · UniProt Q15843
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