Research workbench
Diphtheria tox repressor (C102D mutant) complexed with nickel and dtxr consensus binding sequence
Analyse Diphtheria tox repressor (C102D mutant) complexed with nickel and dtxr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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