MolNFT v1 · #115180 · protein + DNA
Ancmr DNA binding domain - (+)gre complex
5CBZ: “Ancmr DNA binding domain - (+)gre complex”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.82). MolNFT v1 #115180 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CBZ
- Type
- protein + DNA
- Length
- 368 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancmr DNA binding domain; DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G…
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancmr DNA binding domain | protein | 73 | 30% helix, 11% strand | — |
| B | Ancmr DNA binding domain | protein | 74 | 30% helix, 11% strand | — |
| C, G | DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| D, H | DNA (5'- D(*TP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3') | dna | 18 | — | — |
| E | Ancmr DNA binding domain | protein | 76 | 29% helix, 11% strand | — |
| F | Ancmr DNA binding domain | protein | 73 | 32% 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.82 | 0.96 | 30 | empty |
| 2 | 523 | 0.71 | 0.80 | 42 | empty |
| 3 | 633 | 0.69 | 0.78 | 58 | empty |
| 4 | 123 | 0.46 | 0.78 | 22 | empty |
| 5 | 95 | 0.38 | 0.76 | 18 | empty |
Interfaces
16 interfaces between chains.
- C–D · 781 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- G–H · 774 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–E · 702 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 651 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 588 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5CBZ · AncMR 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 5CBZ · PDBe 5CBZ
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