Research workbench
Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase C236Y mutant
Analyse Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase C236Y mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WFZ
- Type
- protein
- Length
- 2,961 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lacto-N-biose phosphorylase
- EC
- 2.4.1.211
- UniProt
- E8MF13
- Ligands
- NDG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 746 | 31% helix, 23% strand | E8MF13 |
| B | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 734 | 31% helix, 24% strand | E8MF13 |
| C | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 744 | 30% helix, 23% strand | E8MF13 |
| D | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 737 | 30% helix, 24% strand | E8MF13 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.81 | 0.89 | 75 | empty |
| 2 | 432 | 0.80 | 0.88 | 71 | empty |
| 3 | 493 | 0.77 | 0.85 | 48 | empty |
| 4 | 459 | 0.77 | 0.85 | 43 | empty |
| 5 | 473 | 0.76 | 0.85 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3412 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3405 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 301 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 193 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3WFZ · Crystal structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase C236Y Mutant · the same entry in another collection · chain D against D, TM-score 1.00
- E8MF13 · AlphaFold monomer V2.0 prediction for 1,3-beta-galactosyl-N- acetylhexosamine… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 E8MF13
- Elsewhere: RCSB PDB 3WFZ · PDBe 3WFZ · UniProt E8MF13
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