MolNFT v1 · #32118 · protein
Crystal structure of HIV-1 tat derived nonapeptides TAT(1-9) bound to the active site of dipeptidyl peptidase IV (CD26)
2BGR: “Crystal structure of HIV-1 tat derived nonapeptides TAT(1-9) bound to the active site of dipeptidyl peptidase…”. X-ray diffraction, 3 ligands (NAG, FUC, BMA), 16 pockets (best druggability 0.75). MolNFT v1 #32118 on GenesisL1: 3D…
- PDB
- 2BGR
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV; HIV-1 tat protein derived N-terminal nonapeptide
- EC
- 3.4.14.5
- UniProt
- P27487, P12506
- Ligands
- NAG, FUC, BMA
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 729 | 17% helix, 37% strand | P27487 |
| Y, Z | HIV-1 tat protein derived N-terminal nonapeptide | protein | 3 | 0% helix, 0% strand | P12506 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.75 | 0.97 | 22 | empty |
| 2 | 982 | 0.73 | 0.76 | 102 | empty |
| 3 | 881 | 0.72 | 0.77 | 92 | empty |
| 4 | 397 | 0.54 | 0.73 | 45 | empty |
| 5 | 234 | 0.53 | 0.76 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2303 Ų buried · 42 hydrogen bonds · protein-protein
- A–Y · 280 Ų buried · 7 hydrogen bonds · protein-protein
- B–Z · 279 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 2BGR · Crystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) bound to the active site of… · the same entry in another collection · chain A against A, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · 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 P27487
- Every structure of UniProt P12506
- Elsewhere: RCSB PDB 2BGR · PDBe 2BGR · UniProt P27487 · UniProt P12506
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