MolNFT v1 · #145979 · protein
Complex structure of ulvan lyase from nonlaben ulvanivorans- NLR48
6D3U: “Complex structure of ulvan lyase from nonlaben ulvanivorans- NLR48”. X-ray diffraction, 5 ligands (83Y, GCD, BDP), 2 pockets (best druggability 0.77). MolNFT v1 #145979 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D3U
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ulvan lyase
- UniProt
- A0A084JZF2
- Ligands
- 83Y, GCD, BDP, CA, PO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ulvan lyase | protein | 260 | 5% helix, 50% strand | A0A084JZF2 |
Ligands and binding sites
- 83Y · 3-O-sulfo-alpha-L-rhamnopyranose · ligand · 4 copies · chains A, B
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.77 | 0.80 | 101 | 83Y, PO4, EDO |
| 2 | 80 | 0.55 | 0.86 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6D3U · Complex structure of Ulvan lyase from Nonlaben Ulvanivorans- NLR48 · 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 A0A084JZF2
- Elsewhere: RCSB PDB 6D3U · PDBe 6D3U · UniProt A0A084JZF2
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