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Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase in complex with galnac
Analyse Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZUT
- Type
- protein
- Length
- 2,962 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
- Q5NU17
- Ligands
- A2G, MG, NO3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 744 | 31% helix, 24% strand | Q5NU17 |
| B | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 735 | 31% helix, 24% strand | Q5NU17 |
| D | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 739 | 31% helix, 24% strand | Q5NU17 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · chains A
- GOL · Glycerol · additive · 9 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 | 453 | 0.81 | 0.89 | 77 | empty |
| 2 | 465 | 0.80 | 0.88 | 76 | empty |
| 3 | 468 | 0.77 | 0.85 | 45 | empty |
| 4 | 456 | 0.76 | 0.85 | 41 | MG |
| 5 | 442 | 0.76 | 0.85 | 41 | MG |
Interfaces
5 interfaces between chains.
- C–D · 3426 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3422 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 301 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 199 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2ZUT · Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GalNAc · 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 Q5NU17
- Elsewhere: RCSB PDB 2ZUT · PDBe 2ZUT · UniProt Q5NU17
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