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Crystal structure of catalytic domain of human BETA1, 4GALACTOSYLTRANSFERASE 7 in closed conformation in complex with manganese and udp
Analyse Crystal structure of catalytic domain of human BETA1, 4GALACTOSYLTRANSFERASE 7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IRQ
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,4-galactosyltransferase 7
- EC
- 2.4.1.-, 2.4.1.133
- UniProt
- Q9UBV7
- Ligands
- UDP, MN
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-, 2.4.1.133) | protein | 246 | 22% helix, 24% strand | Q9UBV7 |
| B | Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-, 2.4.1.133) | protein | 240 | 22% helix, 23% strand | Q9UBV7 |
| C | Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-, 2.4.1.133) | protein | 249 | 22% helix, 23% strand | Q9UBV7 |
| D | Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-, 2.4.1.133) | protein | 243 | 23% helix, 23% strand | Q9UBV7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.82 | 0.87 | 75 | MN, UDP, TRS |
| 2 | 302 | 0.80 | 0.91 | 35 | MN, UDP, TRS |
| 3 | 458 | 0.80 | 0.88 | 56 | MN, UDP, TRS |
| 4 | 319 | 0.79 | 0.89 | 37 | MN, UDP, TRS |
| 5 | 144 | 0.62 | 0.85 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 980 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 537 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 256 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 241 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4IRQ · Crystal structure of catalytic domain of human beta1,4galactosyltransferase 7 in closed… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UBV7 · AlphaFold monomer V2.0 prediction for beta-1,4-galactosyltransferase 7 (Q9UBV7) · a predicted model of the same protein · chain A 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 Q9UBV7
- Elsewhere: RCSB PDB 4IRQ · PDBe 4IRQ · UniProt Q9UBV7
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