MolNFT v1 · #50141 · protein + DNA
Polymerase domain from mycobacterium tuberculosis ligase D in complex with DNA
2R9L · DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3'): “Polymerase domain from mycobacterium tuberculosis ligase D in complex with DNA”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #50141 on GenesisL1: 3D structure, binding sites…
- PDB
- 2R9L
- Type
- protein + DNA
- Length
- 603 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3'); DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA…
- EC
- 2.7.7.-
- UniProt
- P71571
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3') | dna | 5 | — | — |
| D | DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3') | dna | 11 | — | — |
| F | DNA (5'- D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3') | dna | 13 | — | — |
| A | Putative DNA ligase-like protein (EC 2.7.7.-) | protein | 287 | 29% helix, 28% strand | P71571 |
| B | Putative DNA ligase-like protein (EC 2.7.7.-) | protein | 282 | 30% helix, 28% strand | P71571 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.73 | 0.78 | 55 | EDO |
| 2 | 517 | 0.72 | 0.81 | 48 | EDO |
| 3 | 153 | 0.50 | 0.79 | 24 | empty |
| 4 | 148 | 0.47 | 0.77 | 22 | empty |
| 5 | 65 | 0.33 | 0.77 | 16 | empty |
Interfaces
9 interfaces between chains.
- F–B · 595 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 548 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–F · 425 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- C–A · 312 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–B · 300 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 2R9L · Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA · the same entry in another collection · chain C against C, 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 P71571
- Elsewhere: RCSB PDB 2R9L · PDBe 2R9L · UniProt P71571
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.