MolNFT v1 · #142434 · protein + DNA
Structure of TREX2 in complex with a duplex DNA with 2 nucleotide 3'- overhang
6A4B · Three prime repair exonuclease 2: “Structure of TREX2 in complex with a duplex DNA with 2 nucleotide 3'- overhang”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.66). MolNFT v1 #142434 on GenesisL1: 3D structure…
- PDB
- 6A4B
- Type
- protein + DNA
- Length
- 1,385 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Three prime repair exonuclease 2; DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)…
- EC
- 3.1.11.2
- UniProt
- Q9R1A9
- Ligands
- MG
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 9 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 213 | 42% helix, 19% strand | Q9R1A9 |
| B | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 216 | 43% helix, 18% strand | Q9R1A9 |
| C | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 215 | 38% helix, 16% strand | Q9R1A9 |
| D | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 215 | 40% helix, 15% strand | Q9R1A9 |
| E | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 217 | 43% helix, 18% strand | Q9R1A9 |
| F | Three prime repair exonuclease 2 (EC 3.1.11.2) | protein | 217 | 44% helix, 16% strand | Q9R1A9 |
| G, H, I, L | DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)- 3') | dna | 15 | — | — |
| J | DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)- 3') | dna | 18 | — | — |
| K | DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)- 3') | dna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 11 copies · chains A, H, B, G, C, I, D, J, E, K, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.66 | 0.77 | 54 | MG |
| 2 | 374 | 0.61 | 0.77 | 38 | empty |
| 3 | 268 | 0.59 | 0.79 | 40 | empty |
| 4 | 435 | 0.58 | 0.74 | 40 | empty |
| 5 | 401 | 0.57 | 0.75 | 40 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1555 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1547 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 1508 Ų buried · 40 hydrogen bonds · protein-protein
- E–K · 809 Ų buried · 17 hydrogen bonds · protein-nucleic
- F–L · 752 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6A4B · Structure of TREX2 in complex with a duplex DNA with 2 nucleotide 3'-overhang · the same entry in another collection · chain L against L, 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 Q9R1A9
- Elsewhere: RCSB PDB 6A4B · PDBe 6A4B · UniProt Q9R1A9
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