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Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant)
Analyse Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IXF
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen peptide transporter 1
- UniProt
- P36370
- Ligands
- ATP, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Antigen peptide transporter 1 | protein | 255 | 36% helix, 23% strand | P36370 |
| C | Antigen peptide transporter 1 | protein | 252 | 36% helix, 23% strand | P36370 |
| D | Antigen peptide transporter 1 | protein | 250 | 37% helix, 24% strand | P36370 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.77 | 0.79 | 112 | ATP, MG, GOL |
| 2 | 1082 | 0.75 | 0.78 | 114 | ATP, MG |
| 3 | 323 | 0.65 | 0.81 | 38 | empty |
| 4 | 269 | 0.58 | 0.79 | 45 | empty |
| 5 | 162 | 0.47 | 0.76 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 924 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 396 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2IXF · Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant) · the same entry in another collection · chain A against A, TM-score 1.00
- P36370 · AlphaFold monomer V2.0 prediction for antigen peptide transporter 1 (P36370) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P36370
- Elsewhere: RCSB PDB 2IXF · PDBe 2IXF · UniProt P36370
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