MolNFT v1 · #117093 · protein + DNA
Crystal of amtr from corynebacterium glutamicum in complex with DNA
5DY0 · Tetr family transcriptional regulator: “Crystal of amtr from corynebacterium glutamicum in complex with DNA”. X-ray diffraction, 14 pockets (best druggability 0.76). MolNFT v1 #117093 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DY0
- Type
- protein + DNA
- Length
- 979 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetr family transcriptional regulator; DNA
- UniProt
- A0A072Z681
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetr family transcriptional regulator | protein | 220 | 66% helix, 0% strand | A0A072Z681 |
| B | Tetr family transcriptional regulator | protein | 218 | 62% helix, 0% strand | A0A072Z681 |
| C | Tetr family transcriptional regulator | protein | 218 | 66% helix, 0% strand | A0A072Z681 |
| D | Tetr family transcriptional regulator | protein | 219 | 67% helix, 0% strand | A0A072Z681 |
| E, F, G, H | DNA | dna | 26 | — | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.76 | 0.78 | 107 | empty |
| 2 | 766 | 0.75 | 0.80 | 62 | empty |
| 3 | 740 | 0.73 | 0.79 | 65 | empty |
| 4 | 500 | 0.61 | 0.75 | 42 | empty |
| 5 | 339 | 0.51 | 0.73 | 27 | empty |
Interfaces
16 interfaces between chains.
- E–F · 1122 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- G–H · 1103 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- C–D · 826 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 819 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 602 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5DY0 · Crystal of AmtR from Corynebacterium glutamicum in complex with 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 A0A072Z681
- Elsewhere: RCSB PDB 5DY0 · PDBe 5DY0 · UniProt A0A072Z681
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