Research workbench
DNA binding protein and DNA complex structure
Analyse DNA binding protein and DNA complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KPY
- Type
- protein + DNA
- Length
- 1,415 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T…
- UniProt
- Q746M7
- Ligands
- DT, MN
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 676 | 29% helix, 31% strand | Q746M7 |
| B | Uncharacterized protein | protein | 675 | 29% helix, 31% strand | Q746M7 |
| C, E | DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- 3') | dna | 16 | — | — |
| D, F | DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') | dna | 10 | — | — |
| M, N | DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3') | dna | 6 | — | — |
Ligands and binding sites
- DT · Thymidine-5'-monophosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, D, N, B, F, M, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.82 | 0.85 | 59 | empty |
| 2 | 1183 | 0.81 | 0.83 | 68 | empty |
| 3 | 791 | 0.71 | 0.77 | 79 | empty |
| 4 | 337 | 0.66 | 0.80 | 37 | DT |
| 5 | 405 | 0.65 | 0.79 | 47 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2509 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1722 Ų buried · 50 hydrogen bonds · protein-nucleic
- B–E · 1708 Ų buried · 46 hydrogen bonds · protein-nucleic
- B–F · 960 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 948 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 4KPY · DNA binding protein and DNA complex structure · 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 Q746M7
- Elsewhere: RCSB PDB 4KPY · PDBe 4KPY · UniProt Q746M7
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