Research workbench
Cryo-EM structure of the human tap ATP-binding cassette transporter
Analyse Cryo-EM structure of the human tap ATP-binding cassette transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U1D
- Type
- protein
- Length
- 1,168 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen peptide transporter 1; Antigen peptide transporter 2; Tap transporter inhibitor…
- UniProt
- Q03518, Q03519, A0A140GKJ0
- Pockets
- 19 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 67% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen peptide transporter 1 | protein | 561 | 67% helix, 9% strand | Q03518 |
| B | Antigen peptide transporter 2 | protein | 552 | 67% helix, 7% strand | Q03519 |
| X | Tap transporter inhibitor ICP47 | protein | 55 | 62% helix, 2% strand | A0A140GKJ0 |
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.88 | 0.91 | 117 | empty |
| 2 | 959 | 0.85 | 0.87 | 150 | empty |
| 3 | 1054 | 0.80 | 0.81 | 118 | empty |
| 4 | 234 | 0.79 | 0.92 | 33 | empty |
| 5 | 655 | 0.76 | 0.82 | 67 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4052 Ų buried · 25 hydrogen bonds · protein-protein
- B–X · 1804 Ų buried · 19 hydrogen bonds · protein-protein
- A–X · 771 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5U1D · Cryo-EM structure of the human TAP ATP-Binding Cassette Transporter · the same entry in another collection · chain X against X, TM-score 1.00
- Q03518 · AlphaFold monomer V2.0 prediction for antigen peptide transporter 1 (Q03518) · a predicted model of the same protein · chain A against A, TM-score 0.90
- Q03519 · AlphaFold monomer V2.0 prediction for antigen peptide transporter 2 (Q03519) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 Q03518
- Every structure of UniProt Q03519
- Every structure of UniProt A0A140GKJ0
- Elsewhere: RCSB PDB 5U1D · PDBe 5U1D · UniProt Q03518 · UniProt Q03519 · UniProt A0A140GKJ0
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