MolNFT v1 · #165939 · protein
Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from lentinula edodes (LEGH128_IV)
6UB2: “Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from lentinula edodes (LEGH128_IV)”. X-ray diffraction, 2 ligands (CL, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #165939 on GenesisL1: 3D structure…
- PDB
- 6UB2
- Type
- protein
- Length
- 993 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-1,3-glucanase
- UniProt
- G9M5R4
- Ligands
- CL, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-1,3-glucanase | protein | 248 | 35% helix, 19% strand | G9M5R4 |
| B, C | Endo-beta-1,3-glucanase | protein | 249 | 34% helix, 20% strand | G9M5R4 |
| D | Endo-beta-1,3-glucanase | protein | 247 | 34% helix, 20% strand | G9M5R4 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.72 | 0.82 | 61 | MES |
| 2 | 138 | 0.54 | 0.81 | 23 | empty |
| 3 | 129 | 0.49 | 0.79 | 37 | empty |
| 4 | 173 | 0.44 | 0.74 | 22 | MES |
| 5 | 139 | 0.40 | 0.74 | 26 | MES |
Interfaces
5 interfaces between chains.
- A–D · 394 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 189 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 164 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 164 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 147 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UB2 · Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes… · the same entry in another collection · chain C against C, 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 G9M5R4
- Elsewhere: RCSB PDB 6UB2 · PDBe 6UB2 · UniProt G9M5R4
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