Research workbench
Crystal structure of rhamnogalacturonan lyase yesw at 1.40 a resolution
Analyse Crystal structure of rhamnogalacturonan lyase yesw at 1.40 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z8R
- Type
- protein
- Length
- 1,166 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yesw protein
- EC
- 4.2.2.-
- UniProt
- O31526
- Ligands
- CA
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Yesw protein (EC 4.2.2.-) | protein | 583 | 4% helix, 37% strand | O31526 |
Ligands and binding sites
- CA · Calcium ion · metal · 20 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.58 | 0.77 | 43 | empty |
| 2 | 268 | 0.58 | 0.78 | 37 | MPD |
| 3 | 356 | 0.53 | 0.73 | 40 | empty |
| 4 | 136 | 0.50 | 0.79 | 21 | MPD |
| 5 | 177 | 0.50 | 0.77 | 31 | MPD |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2Z8R · Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- O31526 · AlphaFold monomer V2.0 prediction for rhamnogalacturonan endolyase yesw (O31526) · a predicted model of the same protein · 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 O31526
- Elsewhere: RCSB PDB 2Z8R · PDBe 2Z8R · UniProt O31526
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