Research workbench
Post catalytic complex of prim-polc from mycobacterium smegmatis with gapped DNA and 3'-dutp
Analyse Post catalytic complex of prim-polc from mycobacterium smegmatis with gapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SA1
- Type
- protein + DNA
- Length
- 713 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase ligd, polymerase domain; DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3'); DNA…
- UniProt
- A0R5T1
- Ligands
- U3H, PPV, MN, MG, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase ligd, polymerase domain | protein | 328 | 32% helix, 21% strand | A0R5T1 |
| B, E | DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3') | dna | 7 | — | — |
| C | DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3') | dna | 13 | — | — |
| H | DNA (5'-D(P*TP*GP*CP*GP*(DUI))-3') | dna | 5 | — | — |
| D | DNA polymerase ligd, polymerase domain | protein | 331 | 32% helix, 21% strand | A0R5T1 |
| F | DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3') | dna | 15 | — | — |
| G | DNA (5'-D(P*TP*GP*CP*GP*(DUI))-3') | dna | 7 | — | — |
Ligands and binding sites
- U3H · 3'-deoxy-uridine 5'-triphosphate · ligand · chains A, C, H
- PPV · Pyrophosphate · ligand · chains D
- MN · Manganese (II) ion · metal · 4 copies · chains A, D
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.75 | 0.78 | 86 | EDO |
| 2 | 607 | 0.68 | 0.77 | 53 | MN, U3H |
| 3 | 601 | 0.68 | 0.77 | 49 | MN, PPV, EDO |
| 4 | 187 | 0.54 | 0.79 | 26 | empty |
| 5 | 160 | 0.53 | 0.80 | 25 | empty |
Interfaces
11 interfaces between chains.
- A–C · 585 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–F · 580 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–G · 378 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- A–D · 376 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 374 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 6SA1 · Post catalytic complex of Prim-PolC from Mycobacterium smegmatis with gapped DNA and… · the same entry in another collection · chain A against A, 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 A0R5T1
- Elsewhere: RCSB PDB 6SA1 · PDBe 6SA1 · UniProt A0R5T1
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