Research workbench
Truncated version of chaetomium thermophilum udp-glucose glucosyl transferase (uggt) lacking domain TRXL2 (417-650).
Analyse Truncated version of chaetomium thermophilum udp-glucose glucosyl transferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TS2
- Type
- protein
- Length
- 4,467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose-glycoprotein glucosyltransferase-like protein, udp-glucose-glycoprotein…
- UniProt
- G0SB58
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose-glycoprotein glucosyltransferase-like protein, udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 1111 | 36% helix, 20% strand | G0SB58 |
| B | Udp-glucose-glycoprotein glucosyltransferase-like protein, udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 1120 | 31% helix, 16% strand | G0SB58 |
| C | Udp-glucose-glycoprotein glucosyltransferase-like protein, udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 1113 | 32% helix, 16% strand | G0SB58 |
| D | Udp-glucose-glycoprotein glucosyltransferase-like protein, udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 1123 | 33% helix, 17% strand | G0SB58 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 4 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 | 418 | 0.81 | 0.90 | 38 | empty |
| 2 | 1170 | 0.81 | 0.82 | 114 | empty |
| 3 | 519 | 0.80 | 0.86 | 65 | empty |
| 4 | 592 | 0.78 | 0.84 | 53 | empty |
| 5 | 78 | 0.77 | 0.99 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 2518 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1972 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 421 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 239 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 223 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6TS2 · Truncated version of Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT)… · 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 G0SB58
- Elsewhere: RCSB PDB 6TS2 · PDBe 6TS2 · UniProt G0SB58
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