Research workbench
Hairpin forming complex, RAG1/2-nicked 12RSS/23RSS complex in CA2+
Analyse Hairpin forming complex, RAG1/2-nicked 12RSS/23RSS complex in CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZDZ
- Type
- protein + DNA
- Length
- 2,239 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mouse RAG1; Mouse RAG2; HMGB1 a-B box; DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*T…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784, P63158
- Ligands
- CA, ZN, K
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mouse RAG1 (EC 3.1.-.-, 2.3.2.27) | protein | 618 | 52% helix, 11% strand | P15919 |
| B | Mouse RAG2 | protein | 341 | 4% helix, 49% strand | P21784 |
| C | Mouse RAG1 (EC 3.1.-.-, 2.3.2.27) | protein | 623 | 52% helix, 12% strand | P15919 |
| D | Mouse RAG2 | protein | 340 | 3% helix, 47% strand | P21784 |
| N | HMGB1 a-B box | protein | 117 | 78% helix, 0% strand | P63158 |
| F | DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)- 3') | dna | 45 | — | — |
| I | DNA (54-mer) | dna | 16 | — | — |
| J | DNA (30-mer) | dna | 16 | — | — |
| G | DNA (39-mer) | dna | 54 | — | — |
| L | DNA chain L | dna | 30 | — | — |
| M | DNA chain M | dna | 39 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, F, I, C, G
- ZN · Zinc ion · metal · 2 copies · chains A, C
- K · Potassium ion · metal · 2 copies · chains A, F, L, C, G, M
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, 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 | 468 | 0.83 | 0.90 | 45 | EDO |
| 2 | 1110 | 0.83 | 0.84 | 131 | empty |
| 3 | 694 | 0.81 | 0.85 | 52 | empty |
| 4 | 1170 | 0.81 | 0.83 | 87 | empty |
| 5 | 273 | 0.79 | 0.92 | 44 | empty |
Interfaces
25 interfaces between chains.
- A–C · 4144 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1972 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1958 Ų buried · 41 hydrogen bonds · protein-protein
- G–M · 1678 Ų buried · 130 hydrogen bonds · nucleic-nucleic
- F–L · 1279 Ų buried · 110 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ZDZ · Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+ · 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 D 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 P63158
- Elsewhere: RCSB PDB 5ZDZ · PDBe 5ZDZ · UniProt P15919 · UniProt P21784 · UniProt P63158
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