MolNFT v1 · #99277 · protein
Crystal structure of glycoside hydrolase family 5 mannosidase from rhizomucor miehei
4LYP · Exo-beta-1,4-mannosidase: “Crystal structure of glycoside hydrolase family 5 mannosidase from rhizomucor miehei”. X-ray diffraction, 1 ligand (GAI), 3 pockets (best druggability 0.69). MolNFT v1 #99277 on GenesisL1: 3D structure…
- PDB
- 4LYP
- Type
- protein
- Length
- 831 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-beta-1,4-mannosidase
- EC
- 3.2.1.25
- Ligands
- GAI
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-beta-1,4-mannosidase (EC 3.2.1.25) | protein | 416 | 42% helix, 14% strand | — |
| B | Exo-beta-1,4-mannosidase (EC 3.2.1.25) | protein | 415 | 41% helix, 14% strand | — |
Ligands and binding sites
- GAI · Guanidine · ligand · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.69 | 0.75 | 104 | empty |
| 2 | 156 | 0.60 | 0.83 | 21 | GAI, TRS |
| 3 | 183 | 0.58 | 0.81 | 28 | GAI, TRS |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4LYP · Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase from Rhizomucor miehei · 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
- Elsewhere: RCSB PDB 4LYP · PDBe 4LYP
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