MolNFT v1 · #141121 · protein + DNA
Crystal structure of TREX1 in complex with a duplex DNA with 3' overhang
5YWT · Three-prime repair exonuclease 1: “Crystal structure of TREX1 in complex with a duplex DNA with 3' overhang”. X-ray diffraction, 2 ligands (MG, CO), 3 pockets (best druggability 0.59). MolNFT v1 #141121 on GenesisL1: 3D structure…
- PDB
- 5YWT
- Type
- protein + DNA
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three-prime repair exonuclease 1; DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')
- EC
- 3.1.11.2
- UniProt
- Q91XB0
- Ligands
- MG, CO
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 222 | 40% helix, 17% strand | Q91XB0 |
| B | Three-prime repair exonuclease 1 (EC 3.1.11.2) | protein | 220 | 39% helix, 16% strand | Q91XB0 |
| D | DNA (5'-D(*GP*GP*CP*CP*CP*T)-3') | dna | 6 | — | — |
| C | DNA (5'-D(*GP*GP*CP*CP*CP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
- CO · Cobalt (II) ion · metal · 3 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.59 | 0.76 | 42 | empty |
| 2 | 203 | 0.55 | 0.79 | 17 | empty |
| 3 | 71 | 0.35 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1766 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 710 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 516 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5YWT · Crystal structure of TREX1 in complex with a duplex DNA with 3' overhang · 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 5YWT · PDBe 5YWT · UniProt Q91XB0
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