MolNFT v1 · #100013 · protein + DNA
Polymerase domain from mycobacterium tuberculosis ligase D in complex with an annealed double-strand DNA break.
4MKY · DNA ligase-like protein RV0938/MT0965: “Polymerase domain from mycobacterium tuberculosis ligase D in complex with an annealed double-strand DNA…”. X-ray diffraction, 12 pockets (best druggability 0.83). MolNFT v1 #100013 on…
- PDB
- 4MKY
- Type
- protein + DNA
- Length
- 1,187 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA ligase-like protein RV0938/MT0965; 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'…
- UniProt
- P71571
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | DNA ligase-like protein RV0938/MT0965 | protein | 284 | 30% helix, 28% strand | P71571 |
| B | DNA ligase-like protein RV0938/MT0965 | protein | 283 | 31% helix, 29% strand | P71571 |
| E, G, I, K | 5'-D(P*DGP*DCP*DGP*DGP*DC)-3' | dna | 3 | — | — |
| F, H, J, L | 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3' | dna | 10 | — | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.83 | 0.84 | 128 | empty |
| 2 | 751 | 0.78 | 0.82 | 65 | empty |
| 3 | 572 | 0.73 | 0.81 | 53 | empty |
| 4 | 207 | 0.59 | 0.81 | 28 | empty |
| 5 | 229 | 0.50 | 0.75 | 29 | empty |
Interfaces
23 interfaces between chains.
- C–D · 645 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 444 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–L · 416 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–J · 407 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 4MKY · Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed… · the same entry in another collection · chain G against G, 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 4MKY · PDBe 4MKY · UniProt P71571
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