Research workbench
Cryo-EM structure of the DDB1-DCAF1-CUL4A-RBX1 complex
Analyse Cryo-EM structure of the DDB1-DCAF1-CUL4A-RBX1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OKQ
- Type
- protein
- Length
- 9,028 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; DDB1- and CUL4-associated factor 1; Cullin-4A; E3…
- EC
- 2.7.11.1, 2.3.2.27, 2.3.2.32
- UniProt
- Q16531, Q9Y4B6, Q13619, P62877
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | DNA damage-binding protein 1 | protein | 1135 | 6% helix, 53% strand | Q16531 |
| B, F, J, N | DDB1- and CUL4-associated factor 1 (EC 2.7.11.1) | protein | 331 | 7% helix, 45% strand | Q9Y4B6 |
| C, G, K, O | Cullin-4A | protein | 719 | 62% helix, 7% strand | Q13619 |
| D, H, L, P | E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32) | protein | 72 | 11% helix, 29% strand | P62877 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.85 | 0.87 | 170 | empty |
| 2 | 891 | 0.82 | 0.84 | 134 | empty |
| 3 | 940 | 0.82 | 0.84 | 136 | empty |
| 4 | 677 | 0.81 | 0.86 | 119 | empty |
| 5 | 1084 | 0.81 | 0.83 | 149 | empty |
Interfaces
24 interfaces between chains.
- O–P · 1108 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1105 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1105 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 1104 Ų buried · 28 hydrogen bonds · protein-protein
- M–O · 632 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7OKQ · Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex · the same entry in another collection · chain K against K, 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 Q16531
- Every structure of UniProt Q9Y4B6
- Every structure of UniProt Q13619
- Every structure of UniProt P62877
- Elsewhere: RCSB PDB 7OKQ · PDBe 7OKQ · UniProt Q16531 · UniProt Q9Y4B6 · UniProt Q13619 · UniProt P62877
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