MolNFT v1 · #145255 · protein + DNA
Pre-reaction complex, RAG1(E962Q)/2-NICKED/INTACT 12/23RSS complex in MN2+
6CIM · V(D)J recombination-activating protein 1: “Pre-reaction complex, RAG1(E962Q)/2-NICKED/INTACT 12/23RSS complex in MN2+”. X-ray diffraction, 2 ligands (ZN, MN), 20 pockets (best druggability 0.86). MolNFT v1 #145255 on GenesisL1: 3D…
- PDB
- 6CIM
- Type
- protein + DNA
- Length
- 2,156 residues
- Chains
- 10
- 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 · 10 distinct chains · 36% helix, 24% 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 | 611 | 52% helix, 12% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 340 | 3% helix, 49% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 602 | 52% helix, 13% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 339 | 3% helix, 49% strand | P21784 |
| N | High mobility group protein B1 | protein | 90 | 74% helix, 0% strand | P09429 |
| F | Nicked 12RSS intermediate reverse strand | dna | 35 | — | — |
| I | DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') | dna | 10 | — | — |
| L | Nicked 12RSS intermediate forward strand | dna | 25 | — | — |
| G | Intact 23RSS substrate reverse strand | dna | 52 | — | — |
| J | Intact 23RSS substrate forward strand | dna | 52 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1195 | 0.86 | 0.87 | 82 | empty |
| 2 | 688 | 0.82 | 0.86 | 61 | empty |
| 3 | 712 | 0.81 | 0.85 | 58 | empty |
| 4 | 502 | 0.79 | 0.87 | 63 | MN |
| 5 | 509 | 0.76 | 0.84 | 62 | MN |
Interfaces
22 interfaces between chains.
- A–C · 2477 Ų buried · 8 hydrogen bonds · protein-protein
- G–J · 2283 Ų buried · 147 hydrogen bonds · nucleic-nucleic
- A–B · 1999 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1997 Ų buried · 40 hydrogen bonds · protein-protein
- F–L · 1127 Ų buried · 87 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CIM · Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+ · the same entry in another collection · chain J against J, 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
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 6CIM · PDBe 6CIM · UniProt P15919 · UniProt P21784 · UniProt P09429
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