MolNFT v1 · #4118 · protein + DNA
Diphtheria tox repressor (C102D MUTANT)/TOX DNA operator complex
1DDN · 33 base DNA containing toxin operator: “Diphtheria tox repressor (C102D MUTANT)/TOX DNA operator complex”. X-ray diffraction, 1 ligand (NI), 11 pockets (best druggability 0.57). MolNFT v1 #4118 on GenesisL1: 3D structure, binding…
- PDB
- 1DDN
- Type
- protein + DNA
- Length
- 538 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 33 base DNA containing toxin operator; Diphtheria tox repressor
- UniProt
- P33120
- Ligands
- NI
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 33 base DNA containing toxin operator | dna | 33 | — | — |
| F | 33 base DNA containing toxin operator | dna | 33 | — | — |
| A, B, C, D | Diphtheria tox repressor | protein | 118 | 69% helix, 5% strand | P33120 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.57 | 0.76 | 28 | empty |
| 2 | 269 | 0.51 | 0.75 | 28 | empty |
| 3 | 225 | 0.48 | 0.75 | 26 | empty |
| 4 | 217 | 0.43 | 0.73 | 22 | empty |
| 5 | 207 | 0.42 | 0.72 | 23 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1421 Ų buried · 136 hydrogen bonds · nucleic-nucleic
- C–D · 843 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 841 Ų buried · 10 hydrogen bonds · protein-protein
- E–B · 486 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–D · 481 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1DDN · Diphtheria tox repressor (C102D MUTANT)/TOX DNA operator complex · the same entry in another collection · chain E against E, 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 P33120
- Elsewhere: RCSB PDB 1DDN · PDBe 1DDN · UniProt P33120
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