MolNFT v1 · #2582 · protein + DNA
Crystal structure of the cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal binding sh-like domain
1C0W · DNA (5'- D(P*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*CP*CP*TP*AP*CP*CP…: “Crystal structure of the cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal binding…”. X-ray diffraction, 1 ligand (CO), 8 pockets (best…
- PDB
- 1C0W
- Type
- protein + DNA
- Length
- 784 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*CP*CP*TP*AP*CP*CP*CP*TP*A P*AP*T)-3'); DNA…
- UniProt
- P33120
- Ligands
- CO
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(P*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*CP*CP*TP*AP*CP*CP*CP*TP*A P*AP*T)-3') | dna | 21 | — | — |
| F | DNA (5'- D(P*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*GP*CP*TP*AP*CP*CP*CP*TP*A P*AP*T)-3') | dna | 21 | — | — |
| A | Diphtheria toxin repressor | protein | 173 | 61% helix, 8% strand | P33120 |
| B | Diphtheria toxin repressor | protein | 219 | 48% helix, 17% strand | P33120 |
| C | Diphtheria toxin repressor | protein | 175 | 56% helix, 7% strand | P33120 |
| D | Diphtheria toxin repressor | protein | 175 | 58% helix, 7% strand | P33120 |
Ligands and binding sites
- CO · Cobalt (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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.60 | 0.75 | 41 | empty |
| 2 | 344 | 0.55 | 0.75 | 28 | empty |
| 3 | 246 | 0.53 | 0.76 | 31 | empty |
| 4 | 241 | 0.52 | 0.76 | 31 | empty |
| 5 | 288 | 0.52 | 0.75 | 28 | empty |
Interfaces
11 interfaces between chains.
- E–F · 883 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–B · 824 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 820 Ų buried · 16 hydrogen bonds · protein-protein
- E–B · 415 Ų buried · 10 hydrogen bonds · protein-nucleic
- F–D · 415 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 1C0W · Crystal structure of the cobalt-activated diphtheria toxin repressor-DNA complex reveals… · 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 1C0W · PDBe 1C0W · UniProt P33120
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