MolNFT v1 · #104180 · protein
Crystal structure of the E. COLI dinj-yafq toxin-antitoxin complex
4Q2U · Antitoxin dinj: “Crystal structure of the E. COLI dinj-yafq toxin-antitoxin complex”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.81). MolNFT v1 #104180 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Q2U
- Type
- protein
- Length
- 1,390 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin dinj; MRNA interferase yafq
- EC
- 3.1.-.-
- UniProt
- Q47150, Q47149
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I | Antitoxin dinj | protein | 84 | 56% helix, 14% strand | Q47150 |
| B, D, F, H, J, N, P | MRNA interferase yafq (EC 3.1.-.-) | protein | 90 | 36% helix, 32% strand | Q47149 |
| K, M, O | Antitoxin dinj | protein | 83 | 57% helix, 14% strand | Q47150 |
| L | MRNA interferase yafq (EC 3.1.-.-) | protein | 91 | 35% helix, 32% strand | Q47149 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 49 copies · chains A, E, O, B, G, P, M, J, C, K, D, L, I, F, H, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.81 | 0.86 | 88 | SO4 |
| 2 | 1187 | 0.80 | 0.82 | 141 | SO4 |
| 3 | 610 | 0.78 | 0.84 | 104 | SO4 |
| 4 | 119 | 0.56 | 0.84 | 29 | SO4 |
| 5 | 89 | 0.51 | 0.83 | 20 | SO4 |
Interfaces
42 interfaces between chains.
- A–O · 2232 Ų buried · 23 hydrogen bonds · protein-protein
- E–I · 2205 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 2134 Ų buried · 23 hydrogen bonds · protein-protein
- G–M · 2119 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1630 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4Q2U · Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex · the same entry in another collection · chain K against K, 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 Q47150
- Every structure of UniProt Q47149
- Elsewhere: RCSB PDB 4Q2U · PDBe 4Q2U · UniProt Q47150 · UniProt Q47149
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