MolNFT v1 · #141123 · protein + DNA
Crystal structure of TREX1 in complex with a inosine contained ssdna
5YWV · Three-prime repair exonuclease 1: “Crystal structure of TREX1 in complex with a inosine contained ssdna”. X-ray diffraction, 2 ligands (MG, NA), 3 pockets (best druggability 0.65). MolNFT v1 #141123 on GenesisL1: 3D structure…
- PDB
- 5YWV
- Type
- protein + DNA
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three-prime repair exonuclease 1; Inosine contained ssdna
- EC
- 3.1.11.2
- UniProt
- Q91XB0
- Ligands
- MG, NA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 226 | 39% helix, 17% strand | Q91XB0 |
| B | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 224 | 40% helix, 16% strand | Q91XB0 |
| C, D | Inosine contained ssdna | dna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 4 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.65 | 0.76 | 59 | empty |
| 2 | 53 | 0.42 | 0.83 | 18 | MG |
| 3 | 62 | 0.32 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1742 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 551 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5YWV · Crystal structure of TREX1 in complex with a inosine contained ssDNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q91XB0 · AlphaFold monomer V2.0 prediction for three-prime repair exonuclease 1 (Q91XB0) · a predicted model of the same protein · chain A 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 Q91XB0
- Elsewhere: RCSB PDB 5YWV · PDBe 5YWV · UniProt Q91XB0
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