MolNFT v1 · #40598 · protein
Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant)
2IXF · Antigen peptide transporter 1: “Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant)”. X-ray diffraction, 2 ligands (ATP, MG), 7 pockets (best druggability 0.77). MolNFT v1 #40598 on GenesisL1: 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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