MolNFT v2 · #151540 · protein + DNA
Crystal Structure of C. glutamicum AmtR bound to glnA operator DNA
6GY3 · AmtR protein: “Crystal Structure of C. glutamicum AmtR bound to glnA operator DNA”. X-ray diffraction at 2.68, 7 pockets (best druggability 0.73). MolNFT v2 #151540 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GY3
- Type
- protein + DNA
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.68
- Source
- Corynebacterium glutamicum; SYNTHETIC CONSTRUCT
- Molecule
- AmtR protein; DNA (5'-D(*GP*TP*CP*TP*AP*TP*AP*GP*AP*TP*CP*GP*AP*TP*AP*GP*AP*C)-3'); DNA…
- UniProt
- H7C699
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.68 · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AmtR protein | protein | 202 | 70% helix, 0% strand | H7C699 |
| C | DNA (5'-D(*GP*TP*CP*TP*AP*TP*AP*GP*AP*TP*CP*GP*AP*TP*AP*GP*AP*C)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*GP*TP*CP*TP*AP*TP*CP*GP*AP*TP*CP*TP*AP*TP*AP*GP*AP*C)-3') | dna | 18 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.73 | 0.78 | 62 | empty |
| 2 | 58 | 0.70 | 0.97 | 19 | empty |
| 3 | 471 | 0.56 | 0.73 | 27 | empty |
| 4 | 83 | 0.36 | 0.76 | 19 | empty |
| 5 | 98 | 0.35 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 809 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 775 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–D · 333 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 326 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 297 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6GY3 · Crystal structure of C. glutamicum amtr bound to glna operator DNA · 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 H7C699
- Elsewhere: RCSB PDB 6GY3 · PDBe 6GY3 · UniProt H7C699
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