Research workbench
Crystal structure of wild type ALP1U from the biosynthesis of kinamycins
Analyse Crystal structure of wild type ALP1U from the biosynthesis of kinamycins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KXR
- Type
- protein
- Length
- 1,170 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydrolase
- EC
- 3.3.2.3
- UniProt
- Q1RQU8
- Ligands
- MLT
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative hydrolase (EC 3.3.2.3) | protein | 293 | 45% helix, 19% strand | Q1RQU8 |
| C, D | Putative hydrolase (EC 3.3.2.3) | protein | 292 | 44% helix, 19% strand | Q1RQU8 |
Ligands and binding sites
- MLT · D-malate · ligand · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.74 | 0.78 | 127 | empty |
| 2 | 349 | 0.70 | 0.83 | 38 | MLT |
| 3 | 321 | 0.70 | 0.83 | 37 | empty |
| 4 | 360 | 0.69 | 0.82 | 36 | empty |
| 5 | 373 | 0.68 | 0.81 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1602 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1531 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 217 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KXR · Crystal structure of wild type Alp1U from the biosynthesis of kinamycins · 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 Q1RQU8
- Elsewhere: RCSB PDB 6KXR · PDBe 6KXR · UniProt Q1RQU8
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