MolNFT v1 · #56924 · protein
Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase
2ZUS · Lacto-N-biose phosphorylase: “Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.80). MolNFT v1 #56924 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2ZUS
- Type
- protein
- Length
- 2,982 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
- MG
- Pockets
- 20 · best druggability 0.80
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 | 749 | 30% helix, 24% strand | Q5NU17 |
| B | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 744 | 30% helix, 25% strand | Q5NU17 |
| C | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 744 | 31% helix, 24% strand | Q5NU17 |
| D | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 745 | 31% helix, 23% strand | Q5NU17 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, 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 | 525 | 0.80 | 0.87 | 87 | empty |
| 2 | 521 | 0.80 | 0.87 | 88 | empty |
| 3 | 464 | 0.76 | 0.85 | 43 | empty |
| 4 | 479 | 0.76 | 0.84 | 42 | empty |
| 5 | 470 | 0.76 | 0.84 | 45 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3403 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3400 Ų buried · 70 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 259 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 184 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2ZUS · Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase · 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 2ZUS · PDBe 2ZUS · UniProt Q5NU17
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