MolNFT v1 · #51473 · protein
Structure of a family 2 pectate lyase in complex with trigalacturonic acid
2V8K: “Structure of a family 2 pectate lyase in complex with trigalacturonic acid”. X-ray diffraction, 2 ligands (GTR, ADA), 3 pockets (best druggability 0.70). MolNFT v1 #51473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2V8K
- Type
- protein
- Length
- 543 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- EC
- 4.2.2.2
- Ligands
- GTR, ADA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase (EC 4.2.2.2) | protein | 543 | 44% helix, 14% strand | — |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · chains A
- ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.70 | 0.76 | 71 | ADA, GTR |
| 2 | 284 | 0.65 | 0.81 | 28 | empty |
| 3 | 104 | 0.48 | 0.80 | 18 | empty |
Compared structures
- 2V8K · Structure of a Family 2 Pectate Lyase in Complex with Trigalacturonic Acid · 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
- Elsewhere: RCSB PDB 2V8K · PDBe 2V8K
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