Research workbench
ANCGR2 DNA binding domain - (+)gre complex
Analyse ANCGR2 DNA binding domain - (+)gre complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CBY
- Type
- protein + DNA
- Length
- 184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ANCGR2 DNA binding domain; DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*…
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ANCGR2 DNA binding domain | protein | 76 | 30% helix, 11% strand | — |
| B | ANCGR2 DNA binding domain | protein | 72 | 35% helix, 11% strand | — |
| C | DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.71 | 0.79 | 53 | empty |
| 2 | 91 | 0.34 | 0.75 | 19 | empty |
| 3 | 82 | 0.34 | 0.75 | 19 | empty |
| 4 | 52 | 0.34 | 0.79 | 10 | empty |
Interfaces
6 interfaces between chains.
- C–D · 778 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–B · 606 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 359 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 326 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 301 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5CBY · AncGR2 DNA Binding Domain - (+)GRE Complex · 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
- Elsewhere: RCSB PDB 5CBY · PDBe 5CBY
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