Research workbench
Pre-reaction complex, RAG1(E962Q)/2-INTACT/NICKED 12/23RSS complex in MN2+
Analyse Pre-reaction complex, RAG1(E962Q)/2-INTACT/NICKED 12/23RSS complex in MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CIK
- Type
- protein + DNA
- Length
- 2,147 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 · 37% 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 | 607 | 53% helix, 13% strand | P15919 |
| B | V(D)J recombination-activating protein 2 | protein | 341 | 3% helix, 49% strand | P21784 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 602 | 53% helix, 12% strand | P15919 |
| D | V(D)J recombination-activating protein 2 | protein | 335 | 3% helix, 49% strand | P21784 |
| N | High mobility group protein B1 | protein | 90 | 74% helix, 0% strand | P09429 |
| F | Intact 12RSS substrate reverse strand | dna | 35 | — | — |
| I | Intact 12RSS substrate forward strand | dna | 35 | — | — |
| G | Nicked 23RSS intermediate reverse strand | dna | 51 | — | — |
| J | DNA (5'-D(*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)- 3') | dna | 12 | — | — |
| M | Nicked 23RSS intermediate forward strand | dna | 39 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.86 | 0.87 | 80 | empty |
| 2 | 955 | 0.84 | 0.86 | 118 | MN |
| 3 | 696 | 0.81 | 0.85 | 61 | empty |
| 4 | 749 | 0.81 | 0.85 | 56 | empty |
| 5 | 540 | 0.81 | 0.87 | 63 | MN |
Interfaces
22 interfaces between chains.
- A–C · 2519 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2006 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1941 Ų buried · 41 hydrogen bonds · protein-protein
- G–M · 1721 Ų buried · 121 hydrogen bonds · nucleic-nucleic
- F–I · 1500 Ų buried · 112 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CIK · Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+ · the same entry in another collection · chain M against M, 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 6CIK · PDBe 6CIK · UniProt P15919 · UniProt P21784 · UniProt P09429
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