Research workbench
Ternary complex of prim-polc from mycobacterium smegmatis with 2NT gapped DNA and upnhpp
Analyse Ternary complex of prim-polc from mycobacterium smegmatis with 2NT gapped DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SA0
- Type
- protein + DNA
- Length
- 722 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
- 2KH, MN
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase ligd, polymerase domain | protein | 333 | 31% helix, 21% strand | A0R5T1 |
| B, E | DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3') | dna | 7 | — | — |
| C, F | DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3') | dna | 15 | — | — |
| H, G | DNA (5'-D(P*TP*GP*CP*GP)-3') | dna | 6 | — | — |
Ligands and binding sites
- 2KH · 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine · ligand · 2 copies · chains A, C, H, D, F, G
- MN · Manganese (II) ion · metal · 4 copies · chains A, H, D, G
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D, F
- CAC · Cacodylate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.61 | 0.80 | 25 | 2KH, MN |
| 2 | 294 | 0.60 | 0.79 | 32 | 2KH, MN, CAC, EDO |
| 3 | 262 | 0.55 | 0.77 | 35 | empty |
| 4 | 215 | 0.52 | 0.77 | 23 | empty |
| 5 | 51 | 0.47 | 0.86 | 16 | EDO |
Interfaces
11 interfaces between chains.
- A–C · 815 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–F · 779 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 650 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 399 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–H · 394 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6SA0 · Ternary complex of Prim-PolC from Mycobacterium smegmatis with 2nt gapped DNA and UpNHpp · 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 6SA0 · PDBe 6SA0 · UniProt A0R5T1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.