MolNFT v1 · #111723 · protein
C. bescii family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acid
4YZA: “C. bescii family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acid”. X-ray diffraction, 4 ligands (GTR, X1X, ADA), 2 pockets (best druggability 0.67). MolNFT v1 #111723 on GenesisL1: 3D structure…
- PDB
- 4YZA
- Type
- protein
- Length
- 394 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
- GTR, X1X, ADA, CA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pectate lyase (EC 4.2.2.2) | protein | 198 | 2% helix, 56% strand | B9MKT4 |
| B | Pectate lyase (EC 4.2.2.2) | protein | 196 | 2% helix, 59% strand | B9MKT4 |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · 2 copies · chains A, B
- X1X · alpha-D-talopyranuronic acid · ligand · chains A
- ADA · alpha-D-galactopyranuronic acid · sugar · 12 copies · chains A, B
- CA · Calcium ion · metal · 9 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
- IMD · Imidazole · 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 | 718 | 0.67 | 0.75 | 53 | ADA, CA, GTR |
| 2 | 57 | 0.26 | 0.74 | 17 | ADA, CA |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YZA · C. bescii Family 3 pectate lyase double mutant K108A/Q111A 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 4YZA · PDBe 4YZA · UniProt B9MKT4
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