Research workbench
Crystal structure of staph PARE43KDA in complex with kbd
Analyse Crystal structure of staph PARE43KDA in complex with kbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4URL
- Type
- protein
- Length
- 727 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase IV, B subunit
- EC
- 5.99.1.-
- UniProt
- X5EN43
- Ligands
- XAM
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase IV, B subunit (EC 5.99.1.-) | protein | 364 | 38% helix, 26% strand | X5EN43 |
| B | DNA topoisomerase IV, B subunit (EC 5.99.1.-) | protein | 363 | 38% helix, 26% strand | X5EN43 |
Ligands and binding sites
- XAM · (1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyranosyl)-4-hydroxy-2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl 2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.63 | 0.77 | 55 | empty |
| 2 | 341 | 0.55 | 0.75 | 38 | empty |
| 3 | 155 | 0.51 | 0.79 | 23 | empty |
| 4 | 55 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 579 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4URL · Crystal Structure of Staph ParE43kDa in complex with KBD · 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 X5EN43
- Elsewhere: RCSB PDB 4URL · PDBe 4URL · UniProt X5EN43
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