MolNFT v1 · #56214 · protein
Crystal structure of chondroitin polymerase from escherichia COLI strain K4 (K4CP) complexed with udp-galnac and udp
2Z87 · Chondroitin synthase: “Crystal structure of chondroitin polymerase from escherichia COLI strain K4 (K4CP) complexed with udp-galnac…”. X-ray diffraction, 3 ligands (UD2, UDP, MN), 14 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 2Z87
- Type
- protein
- Length
- 1,192 residues
- Chains
- 2
- 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
- UD2, UDP, MN
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chondroitin synthase (EC 2.4.1.175, 2.4.1.226) | protein | 601 | 32% helix, 21% strand | Q8L0V4 |
| B | Chondroitin synthase (EC 2.4.1.175, 2.4.1.226) | protein | 591 | 31% helix, 20% strand | Q8L0V4 |
Ligands and binding sites
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.64 | 0.75 | 49 | UDP, MN |
| 2 | 407 | 0.64 | 0.78 | 41 | UD2, MN |
| 3 | 73 | 0.62 | 0.90 | 16 | empty |
| 4 | 478 | 0.62 | 0.76 | 42 | UDP, MN |
| 5 | 73 | 0.61 | 0.90 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1108 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2Z87 · Crystal structure of chondroitin polymerase from Escherichia coli strain K4 (K4CP)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8L0V4 · AlphaFold monomer V2.0 prediction for chondroitin synthase (Q8L0V4) · a predicted model of the same protein · chain B 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 2Z87 · PDBe 2Z87 · UniProt Q8L0V4
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