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Crystal structure of chondroitin polymerase from escherichia COLI strain K4 (K4CP) complexed with udp-glcua and udp
Analyse Crystal structure of chondroitin polymerase from escherichia COLI strain K4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z86
- Type
- protein
- Length
- 2,378 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chondroitin synthase
- EC
- 2.4.1.175, 2.4.1.226
- UniProt
- Q8L0V4
- Ligands
- UGA, UDP, MN
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chondroitin synthase (EC 2.4.1.175, 2.4.1.226) | protein | 580 | 31% helix, 20% strand | Q8L0V4 |
| B | Chondroitin synthase (EC 2.4.1.175, 2.4.1.226) | protein | 601 | 31% helix, 19% strand | Q8L0V4 |
| C | Chondroitin synthase (EC 2.4.1.175, 2.4.1.226) | protein | 603 | 32% helix, 20% strand | Q8L0V4 |
| D | Chondroitin synthase (EC 2.4.1.175, 2.4.1.226) | protein | 594 | 32% helix, 20% strand | Q8L0V4 |
Ligands and binding sites
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 6 copies · chains A, B, C, D
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, C
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.68 | 0.94 | 16 | empty |
| 2 | 706 | 0.68 | 0.76 | 46 | UGA, MN |
| 3 | 674 | 0.68 | 0.76 | 48 | UGA, MN |
| 4 | 59 | 0.66 | 0.94 | 15 | empty |
| 5 | 474 | 0.61 | 0.75 | 48 | UDP, MN |
Interfaces
2 interfaces between chains.
- C–D · 1004 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2Z86 · Crystal structure of chondroitin polymerase from Escherichia coli strain K4 (K4CP)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8L0V4 · AlphaFold monomer V2.0 prediction for chondroitin synthase (Q8L0V4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8L0V4
- Elsewhere: RCSB PDB 2Z86 · PDBe 2Z86 · UniProt Q8L0V4
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