Research workbench
Antitoxin phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group
Analyse Antitoxin phd from phage P1 in complex with its operator DNA inverted repeat in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZM2
- Type
- protein + DNA
- Length
- 276 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin phd; DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3'); DNA…
- UniProt
- Q06253
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antitoxin phd | protein | 52 | 50% helix, 33% strand | Q06253 |
| B | Antitoxin phd | protein | 61 | 48% helix, 21% strand | Q06253 |
| C | Antitoxin phd | protein | 55 | 47% helix, 24% strand | Q06253 |
| D | Antitoxin phd | protein | 53 | 49% helix, 25% strand | Q06253 |
| E, G | DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3') | dna | 14 | — | — |
| F | DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3') | dna | 14 | — | — |
| H | DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3') | dna | 13 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.72 | 0.97 | 19 | empty |
| 2 | 237 | 0.59 | 0.80 | 30 | empty |
| 3 | 97 | 0.45 | 0.80 | 20 | empty |
| 4 | 57 | 0.26 | 0.74 | 9 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1337 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1337 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 593 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- G–H · 567 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- D–E · 415 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 4ZM2 · Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a… · 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 4ZM2 · PDBe 4ZM2 · UniProt Q06253
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