MolNFT v1 · #115178 · protein + DNA
Ancgr DNA binding domain - (+)gre complex
5CBX: “Ancgr DNA binding domain - (+)gre complex”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.81). MolNFT v1 #115178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CBX
- Type
- protein + DNA
- Length
- 365 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancgr DNA binding domain; DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G…
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancgr DNA binding domain | protein | 72 | 31% helix, 11% strand | — |
| B, F | Ancgr DNA binding domain | protein | 74 | 30% helix, 11% strand | — |
| C, H | 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, G | DNA (5'- D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| E | Ancgr DNA binding domain | protein | 73 | 30% helix, 11% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.81 | 0.94 | 31 | empty |
| 2 | 478 | 0.70 | 0.81 | 36 | empty |
| 3 | 590 | 0.70 | 0.79 | 56 | empty |
| 4 | 211 | 0.44 | 0.73 | 27 | empty |
| 5 | 92 | 0.36 | 0.75 | 18 | empty |
Interfaces
16 interfaces between chains.
- C–D · 781 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- G–H · 776 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–F · 715 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 627 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 581 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5CBX · AncGR 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 5CBX · PDBe 5CBX
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