Research workbench
Structure of the pksa product template domain in complex with a phosphopantetheine mimetic
Analyse Structure of the pksa product template domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KBZ
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Noranthrone synthase
- EC
- 2.3.1.221
- UniProt
- Q12053
- Ligands
- 3B2
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Noranthrone synthase (EC 2.3.1.221) | protein | 316 | 29% helix, 41% strand | Q12053 |
| B | Noranthrone synthase (EC 2.3.1.221) | protein | 315 | 29% helix, 41% strand | Q12053 |
Ligands and binding sites
- 3B2 · (14R)-14-hydroxy-15,15-dimethyl-1-[5-({[(5-methyl-1,2-oxazol-3-yl)methyl]sulfanyl}methyl)-1,2-oxazol-3-yl]-4,9,13-trioxo-2-thia-5,8,12-triazahexadecan-16-yl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.80 | 0.88 | 43 | 3B2 |
| 2 | 367 | 0.79 | 0.88 | 44 | 3B2 |
| 3 | 98 | 0.49 | 0.81 | 18 | empty |
| 4 | 92 | 0.47 | 0.81 | 16 | empty |
| 5 | 172 | 0.41 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1031 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5KBZ · Structure of the PksA Product Template domain in complex with a phosphopantetheine mimetic · the same entry in another collection · chain A against A, TM-score 1.00
- Q12053 · AlphaFold monomer V2.0 prediction for norsolorinic acid synthase (Q12053) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q12053
- Elsewhere: RCSB PDB 5KBZ · PDBe 5KBZ · UniProt Q12053
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