MolNFT v1 · #64348 · protein + DNA
Complex of MTH0212 and an 8BP dsdna with distorted ends
3G0R · Exodeoxyribonuclease: “Complex of MTH0212 and an 8BP dsdna with distorted ends”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.56). MolNFT v1 #64348 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3G0R
- Type
- protein + DNA
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease; 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*CP*G)-3'…
- EC
- 3.1.11.2
- UniProt
- O26314
- Ligands
- NA
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 255 | 33% helix, 27% strand | O26314 |
| B | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 254 | 30% helix, 26% strand | O26314 |
| G | 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*CP*G)-3' | dna | 10 | — | — |
| K | 5'-D(*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3' | dna | 11 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains G, K
- GOL · Glycerol · additive · 12 copies · chains A, K, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.56 | 0.83 | 27 | empty |
| 2 | 95 | 0.43 | 0.79 | 19 | empty |
| 3 | 84 | 0.41 | 0.79 | 20 | empty |
| 4 | 69 | 0.32 | 0.75 | 15 | GOL |
| 5 | 64 | 0.31 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–K · 579 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–G · 573 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–K · 546 Ų buried · 11 hydrogen bonds · protein-nucleic
- G–K · 529 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–G · 499 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
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 O26314
- Elsewhere: RCSB PDB 3G0R · PDBe 3G0R · UniProt O26314
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