Research workbench
Cryo-EM structure of human oligosaccharyltransferase complex ost-B
Analyse Cryo-EM structure of human oligosaccharyltransferase complex ost-B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S7T
- Type
- protein
- Length
- 2,164 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B…
- EC
- 2.4.99.18
- UniProt
- Q8TCJ2, P0C6T2, P61165, P61803, P04843, P04844, A0A024RAD5, Q9H0U3, Q14165
- Ligands
- KZB, EGY, 0K3, MAN, NAG, BMA, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 10 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B (EC 2.4.99.18) | protein | 706 | 55% helix, 6% strand | Q8TCJ2 |
| B | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 | protein | 33 | 85% helix, 0% strand | P0C6T2 |
| C | Transmembrane protein 258 | protein | 78 | 67% helix, 3% strand | P61165 |
| D | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 | protein | 103 | 83% helix, 0% strand | P61803 |
| E | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | protein | 428 | 7% helix, 47% strand | P04843 |
| F | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 | protein | 250 | 31% helix, 30% strand | P04844 |
| G | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit | protein | 410 | 19% helix, 30% strand | A0A024RAD5 |
| H | Magnesium transporter protein 1 | protein | 112 | 63% helix, 0% strand | Q9H0U3 |
| I | Malectin | protein | 37 | 38% helix, 0% strand | Q14165 |
| K | Peptide | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
- KZB · (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S}, 9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13, 18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol · ligand · 13 copies · chains A, C, I, D, F, E, G
- EGY · (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium · ligand · 10 copies · chains A, B, D, F, H, C, E, G
- 0K3 · (2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains F, G, A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, E, G
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains G, E
- MG · Magnesium ion · metal · 2 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.80 | 0.82 | 67 | MG, 0K3 |
| 2 | 77 | 0.74 | 0.97 | 24 | empty |
| 3 | 825 | 0.73 | 0.78 | 66 | EGY |
| 4 | 592 | 0.69 | 0.78 | 56 | empty |
| 5 | 363 | 0.64 | 0.79 | 27 | KZB |
Interfaces
17 interfaces between chains.
- F–G · 2748 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 2435 Ų buried · 32 hydrogen bonds · protein-protein
- A–H · 2293 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 1721 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1433 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6S7T · Cryo-EM structure of human oligosaccharyltransferase complex OST-B · the same entry in another collection · chain K against K, TM-score 1.00
- P04843 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q8TCJ2 · AlphaFold monomer V2.0 prediction for dolichyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q8TCJ2
- Every structure of UniProt P0C6T2
- Every structure of UniProt P61165
- Every structure of UniProt P61803
- Every structure of UniProt P04843
- Every structure of UniProt P04844
- Every structure of UniProt A0A024RAD5
- Every structure of UniProt Q9H0U3
- Every structure of UniProt Q14165
- Elsewhere: RCSB PDB 6S7T · PDBe 6S7T · UniProt Q8TCJ2 · UniProt P0C6T2 · UniProt P61165 · UniProt P61803 · UniProt P04843 · UniProt P04844 · UniProt A0A024RAD5 · UniProt Q9H0U3 · UniProt Q14165
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