MolNFT v1 · #6216 · protein + DNA
Diphtheria tox repressor (C102D mutant) complexed with nickel and dtxr consensus binding sequence
1F5T · 43MER DNA containing dxtr consensus binding sequence: “Diphtheria tox repressor (C102D mutant) complexed with nickel and dtxr consensus binding sequence”. X-ray diffraction, 1 ligand (NI), 8 pockets (best druggability 0.58). MolNFT…
- PDB
- 1F5T
- Type
- protein + DNA
- Length
- 566 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 43MER DNA containing dxtr consensus binding sequence; Diphtheria toxin repressor
- UniProt
- P33120
- Ligands
- NI
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 43MER DNA containing dxtr consensus binding sequence | dna | 43 | — | — |
| F | 43MER DNA containing dxtr consensus binding sequence | dna | 43 | — | — |
| A, B, C, D | Diphtheria toxin repressor | protein | 120 | 65% helix, 7% 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.58 | 0.76 | 28 | empty |
| 2 | 323 | 0.52 | 0.74 | 30 | empty |
| 3 | 279 | 0.52 | 0.75 | 29 | empty |
| 4 | 282 | 0.51 | 0.75 | 26 | empty |
| 5 | 116 | 0.40 | 0.76 | 13 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1872 Ų buried · 180 hydrogen bonds · nucleic-nucleic
- C–D · 955 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 14 hydrogen bonds · protein-protein
- F–D · 478 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–A · 470 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1F5T · Diphtheria tox repressor (C102D mutant) complexed with nickel and dtxr consensus binding… · 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 1F5T · PDBe 1F5T · UniProt P33120
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