MolNFT v1 · #87073 · protein
Crystal structure of LAMA_E269S from zobellia galactanivorans in complex with a trisaccharide of 1,3-1,4-beta-D-glucan.
4BPZ · Endo-1,3-beta-glucanase, family GH16: “Crystal structure of LAMA_E269S from zobellia galactanivorans in complex with a trisaccharide of…”. X-ray diffraction, 3 ligands (BGC, GLC, CA), 5 pockets (best druggability 0.63). MolNFT v1…
- PDB
- 4BPZ
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,3-beta-glucanase, family GH16
- EC
- 3.2.1.39
- UniProt
- G0L5X4
- Ligands
- BGC, GLC, CA
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,3-beta-glucanase, family GH16 (EC 3.2.1.39) | protein | 251 | 2% helix, 52% strand | G0L5X4 |
| B | Endo-1,3-beta-glucanase, family GH16 (EC 3.2.1.39) | protein | 252 | 3% helix, 52% strand | G0L5X4 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 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 | 183 | 0.63 | 0.84 | 46 | empty |
| 2 | 200 | 0.60 | 0.81 | 29 | GLC, BGC |
| 3 | 202 | 0.57 | 0.79 | 29 | GLC, BGC |
| 4 | 286 | 0.56 | 0.76 | 39 | empty |
| 5 | 60 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 657 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4BPZ · Crystal structure of lamA_E269S from Zobellia galactanivorans in complex with a… · 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 G0L5X4
- Elsewhere: RCSB PDB 4BPZ · PDBe 4BPZ · UniProt G0L5X4
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