MolNFT v1 · #141630 · protein + DNA
Hairpin complex, RAG1/2-hairpin 12RSS/23RSS complex in 5MM MN2+ for 2 min at 4'C
5ZE2 · Mouse RAG1: “Hairpin complex, RAG1/2-hairpin 12RSS/23RSS complex in 5MM MN2+ for 2 min at 4'C”. X-ray diffraction, 3 ligands (MN, ZN, K), 20 pockets (best druggability 0.83). MolNFT v1 #141630 on GenesisL1: 3D structure, binding…
- PDB
- 5ZE2
- Type
- protein + DNA
- Length
- 2,241 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 (31-mer); DNA (40-mer); DNA (30-mer)
- 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 | 50% helix, 12% strand | P15919 |
| B | Mouse RAG2 | protein | 341 | 5% helix, 48% 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, 48% strand | P21784 |
| N | HMGB1 a-B box | protein | 117 | 78% helix, 0% strand | P63158 |
| I | DNA (31-mer) | dna | 31 | — | — |
| J | DNA (31-mer) | dna | 31 | — | — |
| G | DNA (40-mer) | dna | 40 | — | — |
| L | DNA (30-mer) | dna | 30 | — | — |
| M | DNA (40-mer) | dna | 40 | — | — |
| F | DNA (30-mer) | dna | 30 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, F, C, J, G
- ZN · Zinc ion · metal · 2 copies · chains A, C
- K · Potassium ion · metal · 2 copies · chains A, L, F, 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 | 498 | 0.83 | 0.90 | 41 | EDO |
| 2 | 432 | 0.83 | 0.91 | 55 | empty |
| 3 | 710 | 0.81 | 0.85 | 61 | empty |
| 4 | 421 | 0.80 | 0.89 | 62 | MN |
| 5 | 388 | 0.79 | 0.89 | 59 | empty |
Interfaces
22 interfaces between chains.
- A–C · 4094 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 1969 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1944 Ų buried · 41 hydrogen bonds · protein-protein
- G–M · 1709 Ų buried · 126 hydrogen bonds · nucleic-nucleic
- L–F · 1284 Ų buried · 100 hydrogen bonds · nucleic-nucleic
Compared structures
- 5ZE2 · Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C · the same entry in another collection · chain F against F, 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 0.99
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 5ZE2 · PDBe 5ZE2 · UniProt P15919 · UniProt P21784 · UniProt P63158
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