MolNFT v1 · #111752 · protein
C. bescii family 3 pectate lyase double mutant K108A/R133A in complex with alpha-D-galactopyranuronic acid
4Z06: “C. bescii family 3 pectate lyase double mutant K108A/R133A in complex with alpha-D-galactopyranuronic acid”. X-ray diffraction, 2 ligands (ADA, CA), 1 pocket (best druggability 0.68). MolNFT v1 #111752 on GenesisL1: 3D structure…
- PDB
- 4Z06
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- EC
- 4.2.2.2
- UniProt
- B9MKT4
- Ligands
- ADA, CA
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase (EC 4.2.2.2) | protein | 198 | 2% helix, 58% strand | B9MKT4 |
| B | Pectate lyase (EC 4.2.2.2) | protein | 195 | 2% helix, 58% strand | B9MKT4 |
Ligands and binding sites
- ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.68 | 0.75 | 59 | CA, ADA |
Interfaces
1 interface between chains.
- A–B · 254 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4Z06 · C. bescii Family 3 pectate lyase double mutant K108A/R133A in complex with… · 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
- Every structure of UniProt B9MKT4
- Elsewhere: RCSB PDB 4Z06 · PDBe 4Z06 · UniProt B9MKT4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.