Research workbench
Antitoxin phd from phage P1 in complex with its operator DNA inverted repeat
Analyse Antitoxin phd from phage P1 in complex with its operator DNA inverted repeat in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZM0
- Type
- protein + DNA
- Length
- 275 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin phd; DNA/RNA (5'-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3'); DNA/RNA…
- UniProt
- Q06253
- Ligands
- NA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antitoxin phd | protein | 55 | 49% helix, 31% strand | Q06253 |
| B | Antitoxin phd | protein | 57 | 46% helix, 23% strand | Q06253 |
| D | Antitoxin phd | protein | 54 | 48% helix, 24% strand | Q06253 |
| E | DNA/RNA (5'-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3') | dna | 13 | — | — |
| F | DNA/RNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*A)-3') | dna | 13 | — | — |
| G | DNA/RNA (5'-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3') | dna | 14 | — | — |
| H | DNA/RNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*A)-3') | dna | 14 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains E, F
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · 2 copies · chains A, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.82 | 0.92 | 53 | empty |
| 2 | 64 | 0.33 | 0.77 | 11 | 144 |
| 3 | 55 | 0.30 | 0.76 | 11 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1398 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1214 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 604 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- E–F · 547 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–H · 431 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 4ZM0 · Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat · 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 Q06253
- Elsewhere: RCSB PDB 4ZM0 · PDBe 4ZM0 · UniProt Q06253
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