MolNFT v1 · #15957 · protein
Crystal structure of lactose synthase complex with udp and manganese
1NKH · Alpha-lactalbumin: “Crystal structure of lactose synthase complex with udp and manganese”. X-ray diffraction, 4 ligands (UDP, CA, MN), 6 pockets (best druggability 0.80). MolNFT v1 #15957 on GenesisL1: 3D structure, binding sites…
- PDB
- 1NKH
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-lactalbumin; Beta-1,4-galactosyltransferase
- EC
- 2.4.1.22, 2.4.1.90, 2.4.1.38
- UniProt
- P29752, P08037
- Ligands
- UDP, CA, MN, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-lactalbumin | protein | 123 | 42% helix, 11% strand | P29752 |
| B, D | Beta-1,4-galactosyltransferase (EC 2.4.1.22, 2.4.1.90, 2.4.1.38) | protein | 272 | 26% helix, 22% strand | P08037 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.80 | 0.84 | 75 | PG4, MN, UDP |
| 2 | 735 | 0.80 | 0.83 | 80 | PG4, MN, UDP |
| 3 | 59 | 0.42 | 0.82 | 22 | empty |
| 4 | 132 | 0.40 | 0.74 | 23 | PG4 |
| 5 | 56 | 0.33 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 598 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 400 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1NKH · Crystal structure of Lactose synthase complex with UDP and Manganese · the same entry in another collection · chain A against A, TM-score 1.00
- P08037 · AlphaFold monomer V2.0 prediction for beta-1,4-galactosyltransferase 1 (P08037) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P29752 · AlphaFold monomer V2.0 prediction for alpha-lactalbumin (P29752) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P29752
- Every structure of UniProt P08037
- Elsewhere: RCSB PDB 1NKH · PDBe 1NKH · UniProt P29752 · UniProt P08037
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