Research workbench
MTH0212 in complex with ssdna in space group P32
Analyse MTH0212 in complex with ssdna in space group P32 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G3Y
- Type
- protein + DNA
- Length
- 517 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease; 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'
- EC
- 3.1.11.2
- UniProt
- O26314
- Ligands
- MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 257 | 31% helix, 27% strand | O26314 |
| B | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 256 | 31% helix, 27% strand | O26314 |
| I | 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3' | dna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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 | 758 | 0.69 | 0.76 | 64 | empty |
| 2 | 202 | 0.54 | 0.79 | 31 | MG |
| 3 | 131 | 0.41 | 0.75 | 26 | MG |
Interfaces
2 interfaces between chains.
- B–I · 455 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
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 3G3Y · PDBe 3G3Y · UniProt O26314
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