MolNFT v1 · #145254 · protein + DNA
Pre-reaction complex, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS complex in MN2+
6CIL · V(D)J recombination-activating protein 1: “Pre-reaction complex, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS complex in MN2+”. X-ray diffraction, 2 ligands (ZN, MN), 20 pockets (best druggability 0.86). MolNFT v1 #145254 on GenesisL1: 3D…
- PDB
- 6CIL
- Type
- protein + DNA
- Length
- 2,076 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V(D)J recombination-activating protein 1; V(D)J recombination-activating protein 2; High…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784, P09429
- Ligands
- ZN, MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 35% helix, 25% 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 | 585 | 51% helix, 12% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 337 | 3% helix, 51% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 589 | 51% helix, 12% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 330 | 3% helix, 49% strand | P21784 |
| N | High mobility group protein B1 | protein | 55 | 78% helix, 0% strand | P09429 |
| F | Intact 12RSS substrate reverse strand | dna | 37 | — | — |
| I | Intact 12RSS substrate forward strand | dna | 37 | — | — |
| G | Intact 23RSS substrate reverse strand | dna | 53 | — | — |
| J | Intact 23RSS substrate forward strand | dna | 53 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, C, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.86 | 0.89 | 59 | empty |
| 2 | 729 | 0.81 | 0.85 | 67 | empty |
| 3 | 725 | 0.81 | 0.85 | 66 | empty |
| 4 | 719 | 0.79 | 0.84 | 72 | MN |
| 5 | 416 | 0.75 | 0.85 | 49 | empty |
Interfaces
19 interfaces between chains.
- G–J · 2289 Ų buried · 144 hydrogen bonds · nucleic-nucleic
- A–C · 2133 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1988 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1903 Ų buried · 35 hydrogen bonds · protein-protein
- F–I · 1633 Ų buried · 93 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CIL · Pre-reaction complex, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS complex in MN2+ · 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 1.00
- P15919 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (P15919) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 6CIL · PDBe 6CIL · UniProt P15919 · UniProt P21784 · UniProt P09429
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