Research workbench
Crystal structure of DMC1GALT1 in complex with udp-MN2+ and the apd- tgalnac-rp
Analyse Crystal structure of DMC1GALT1 in complex with udp-MN2+ and the apd- tgalnac-rp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q4I
- Type
- protein
- Length
- 570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein-N-acetylgalactosamine 3-beta- galactosyltransferase 1; Mucin-1
- EC
- 2.4.1.122
- UniProt
- Q7K237, P15941
- Ligands
- UDP, A2G, MN
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein-N-acetylgalactosamine 3-beta- galactosyltransferase 1 (EC 2.4.1.122) | protein | 279 | 35% helix, 16% strand | Q7K237 |
| B | Glycoprotein-N-acetylgalactosamine 3-beta- galactosyltransferase 1 (EC 2.4.1.122) | protein | 281 | 35% helix, 16% strand | Q7K237 |
| G, F | Mucin-1 | protein | 5 | 0% helix, 0% strand | P15941 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, F, B, G
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains B, G, A, F
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.66 | 0.82 | 37 | UDP, MN, A2G |
| 2 | 310 | 0.66 | 0.81 | 39 | UDP, EDO, A2G |
| 3 | 80 | 0.64 | 0.91 | 22 | empty |
| 4 | 87 | 0.63 | 0.90 | 23 | empty |
| 5 | 168 | 0.59 | 0.82 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2374 Ų buried · 36 hydrogen bonds · protein-protein
- B–G · 333 Ų buried · 1 hydrogen bond · protein-protein
- A–F · 252 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan, 2 modified (disulfide, O-glycosylation, nonstandard).
Compared structures
- 7Q4I · Crystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the APD-TGalNAc-RP · the same entry in another collection · chain A against A, TM-score 1.00
- Q7K237 · AlphaFold monomer V2.0 prediction for glycoprotein-N- acetylgalactosamine… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P15941 · AlphaFold monomer V2.0 prediction for mucin-1 (P15941) · a predicted model of the same protein · chain G against A, TM-score 0.79
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 Q7K237
- Every structure of UniProt P15941
- Elsewhere: RCSB PDB 7Q4I · PDBe 7Q4I · UniProt Q7K237 · UniProt P15941
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