MolNFT v1 · #145163 · protein + DNA
Cryo-EM structure of mouse RAG1/2 hfc complex (3.17 a)
6CG0 · V(D)J recombination-activating protein 1: “Cryo-EM structure of mouse RAG1/2 hfc complex (3.17 a)”. Electron microscopy, 2 ligands (ZN, CA), 20 pockets (best druggability 0.88). MolNFT v1 #145163 on GenesisL1: 3D structure, binding…
- PDB
- 6CG0
- Type
- protein + DNA
- Length
- 2,201 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V(D)J recombination-activating protein 1; V(D)J recombination-activating protein 2; DNA…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784, P09429
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 11 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 614 | 49% helix, 9% strand | P15919 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 616 | 50% helix, 11% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 342 | 2% helix, 42% strand | P21784 |
| B | V(D)J recombination-activating protein 2 | protein | 342 | 3% helix, 45% strand | P21784 |
| F | DNA (46-mer) | dna | 46 | — | — |
| I | DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)- 3') | dna | 16 | — | — |
| J | DNA (5'- D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') | dna | 19 | — | — |
| G | DNA (60-mer) | dna | 60 | — | — |
| L | DNA (30-mer) | dna | 30 | — | — |
| M | DNA (41-mer) | dna | 41 | — | — |
| N | High mobility group protein B1 | protein | 75 | 60% helix, 0% strand | P09429 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, F, C, J, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.88 | 0.89 | 124 | empty |
| 2 | 809 | 0.84 | 0.87 | 68 | empty |
| 3 | 809 | 0.83 | 0.85 | 64 | empty |
| 4 | 1142 | 0.82 | 0.84 | 125 | CA |
| 5 | 80 | 0.72 | 0.96 | 23 | empty |
Interfaces
25 interfaces between chains.
- A–C · 3915 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2040 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1957 Ų buried · 35 hydrogen bonds · protein-protein
- G–M · 1848 Ų buried · 164 hydrogen bonds · nucleic-nucleic
- F–L · 1351 Ų buried · 92 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CG0 · Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A) · the same entry in another collection · chain N against N, TM-score 1.00
- P21784 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 2 (P21784) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P15919
- Every structure of UniProt P21784
- Every structure of UniProt P09429
- Elsewhere: RCSB PDB 6CG0 · PDBe 6CG0 · UniProt P15919 · UniProt P21784 · UniProt P09429
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