Research workbench
The crystal structure of apo arna features an unexpected central binding pocket and provides an explanation for enzymatic coop- erativity
Analyse The crystal structure of apo arna features an unexpected central binding pocket… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WKG
- Type
- protein
- Length
- 3,837 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional polymyxin resistance protein arna
- EC
- 2.1.2.13, 1.1.1.305
- UniProt
- P77398
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional polymyxin resistance protein arna (EC 2.1.2.13, 1.1.1.305) | protein | 636 | 37% helix, 22% strand | P77398 |
| B, E | Bifunctional polymyxin resistance protein arna (EC 2.1.2.13, 1.1.1.305) | protein | 643 | 37% helix, 22% strand | P77398 |
| C | Bifunctional polymyxin resistance protein arna (EC 2.1.2.13, 1.1.1.305) | protein | 637 | 37% helix, 22% strand | P77398 |
| D | Bifunctional polymyxin resistance protein arna (EC 2.1.2.13, 1.1.1.305) | protein | 641 | 38% helix, 23% strand | P77398 |
| F | Bifunctional polymyxin resistance protein arna (EC 2.1.2.13, 1.1.1.305) | protein | 637 | 38% helix, 23% strand | P77398 |
Ligands and binding sites
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.82 | 0.83 | 94 | empty |
| 2 | 959 | 0.82 | 0.83 | 90 | empty |
| 3 | 983 | 0.81 | 0.82 | 89 | empty |
| 4 | 931 | 0.81 | 0.83 | 92 | empty |
| 5 | 1139 | 0.77 | 0.79 | 90 | empty |
Interfaces
12 interfaces between chains.
- B–E · 2245 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2161 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2126 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 717 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 709 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4WKG · The crystal structure of apo ArnA features an unexpected central binding pocket and… · the same entry in another collection · chain F against F, TM-score 1.00
- P77398 · AlphaFold monomer V2.0 prediction for bifunctional polymyxin resistance protein arna… · a predicted model of the same protein · chain F against A, TM-score 0.87
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 P77398
- Elsewhere: RCSB PDB 4WKG · PDBe 4WKG · UniProt P77398
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.