MolNFT v1 · #112996 · protein
Family 2 pectate lyase from vibrio vulnificus
5A29 · Exopolygalacturonate lyase: “Family 2 pectate lyase from vibrio vulnificus”. X-ray diffraction, 2 ligands (SRT, MN), 5 pockets (best druggability 0.83). MolNFT v1 #112996 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5A29
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exopolygalacturonate lyase; Pectate lyase
- UniProt
- Q7MCK3
- Ligands
- SRT, MN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exopolygalacturonate lyase | protein | 548 | 44% helix, 12% strand | Q7MCK3 |
| B | Pectate lyase | protein | 18 | 0% helix, 0% strand | — |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 3 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.83 | 0.86 | 67 | EDO, SRT |
| 2 | 70 | 0.66 | 0.93 | 19 | SRT |
| 3 | 216 | 0.58 | 0.80 | 35 | EDO |
| 4 | 207 | 0.52 | 0.77 | 29 | EDO, SRT |
| 5 | 59 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5A29 · Family 2 Pectate Lyase from Vibrio vulnificus · 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 Q7MCK3
- Elsewhere: RCSB PDB 5A29 · PDBe 5A29 · UniProt Q7MCK3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.