MolNFT v1 · #154918 · protein
Crystal structure of GH136 lacto-N-biosidase from eubacterium ramulus - selenomethionine derivative
6KQS: “Crystal structure of GH136 lacto-N-biosidase from eubacterium ramulus - selenomethionine derivative”. X-ray diffraction, 2 ligands (NAG, GAL), 5 pockets (best druggability 0.65). MolNFT v1 #154918 on GenesisL1: 3D structure, binding…
- PDB
- 6KQS
- Type
- protein
- Length
- 620 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lacto-N-biosidase
- UniProt
- U2PDT9
- Ligands
- NAG, GAL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lacto-N-biosidase | protein | 620 | 25% helix, 30% strand | U2PDT9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- GOL · Glycerol · additive · chains A
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 | 356 | 0.65 | 0.80 | 58 | GOL |
| 2 | 412 | 0.60 | 0.75 | 44 | empty |
| 3 | 288 | 0.59 | 0.78 | 39 | NAG, GAL |
| 4 | 314 | 0.54 | 0.74 | 38 | empty |
| 5 | 63 | 0.33 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 6KQS · Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - selenomethionine… · 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 U2PDT9
- Elsewhere: RCSB PDB 6KQS · PDBe 6KQS · UniProt U2PDT9
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