MolNFT v1 · #141629 · protein + DNA
Hairpin forming complex, RAG1/2-nicked 12RSS/23RSS complex in 2MM MN2+ for 10 min at 4'C
5ZE1 · Mouse RAG1: “Hairpin forming complex, RAG1/2-nicked 12RSS/23RSS complex in 2MM MN2+ for 10 min at 4'C”. X-ray diffraction, 3 ligands (MN, ZN, K), 20 pockets (best druggability 0.83). MolNFT v1 #141629 on GenesisL1: 3D structure…
- PDB
- 5ZE1
- 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
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P21784, P63158
- Ligands
- MN, 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 | 51% helix, 11% strand | P15919 |
| B | Mouse RAG2 | protein | 341 | 3% helix, 49% strand | P21784 |
| C | Mouse RAG1 (EC 3.1.-.-, 2.3.2.27) | protein | 623 | 52% helix, 11% strand | P15919 |
| D | Mouse RAG2 | protein | 340 | 3% helix, 49% strand | P21784 |
| N | HMGB1 a-B box | protein | 117 | 77% helix, 0% strand | P63158 |
| F | DNA | dna | 45 | — | — |
| I | DNA | dna | 16 | — | — |
| J | DNA | dna | 16 | — | — |
| G | DNA | dna | 54 | — | — |
| L | DNA | dna | 30 | — | — |
| M | DNA | dna | 39 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, F, I, C, J, 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 · chains A
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 | 481 | 0.83 | 0.90 | 47 | empty |
| 2 | 1124 | 0.82 | 0.83 | 111 | empty |
| 3 | 722 | 0.82 | 0.85 | 64 | empty |
| 4 | 1142 | 0.81 | 0.82 | 80 | empty |
| 5 | 309 | 0.79 | 0.91 | 47 | empty |
Interfaces
25 interfaces between chains.
- A–C · 4096 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 1958 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1943 Ų buried · 43 hydrogen bonds · protein-protein
- G–M · 1692 Ų buried · 128 hydrogen bonds · nucleic-nucleic
- F–L · 1280 Ų buried · 105 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ZE1 · Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C · 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 5ZE1 · PDBe 5ZE1 · UniProt P15919 · UniProt P21784 · UniProt P63158
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