MolNFT v1 · #112459 · protein + DNA
Antitoxin phd from phage P1 in complex with its operator DNA inverted repeat
4ZM0: “Antitoxin phd from phage P1 in complex with its operator DNA inverted repeat”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.82). MolNFT v1 #112459 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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