MolNFT v1 · #69469 · protein
Structural insights into substrate specificity and the anti beta- elimination mechanism of pectate lyase
3KRG: “Structural insights into substrate specificity and the anti beta- elimination mechanism of pectate lyase”. X-ray diffraction, 2 ligands (ADA, CO), 2 pockets (best druggability 0.51). MolNFT v1 #69469 on GenesisL1: 3D structure…
- PDB
- 3KRG
- Type
- protein
- Length
- 399 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- EC
- 4.2.2.2
- UniProt
- P39116
- Ligands
- ADA, CO
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase (EC 4.2.2.2) | protein | 399 | 18% helix, 31% strand | P39116 |
Ligands and binding sites
- ADA · alpha-D-galactopyranuronic acid · sugar · 6 copies · chains A
- CO · Cobalt (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.51 | 0.74 | 42 | ADA |
| 2 | 52 | 0.26 | 0.74 | 14 | empty |
Compared structures
- 3KRG · Structural insights into substrate specificity and the anti beta-elimination mechanism of… · the same entry in another collection · chain A against A, TM-score 1.00
- P39116 · AlphaFold monomer V2.0 prediction for pectate lyase (P39116) · 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 P39116
- Elsewhere: RCSB PDB 3KRG · PDBe 3KRG · UniProt P39116
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