MolNFT v1 · #32114 · protein
HIV-1 tat protein derived N-terminal nonapeptide TRP2-TAT(1-9) bound to the active site of dipeptidyl peptidase IV (CD26)
2BGN: “HIV-1 tat protein derived N-terminal nonapeptide TRP2-TAT(1-9) bound to the active site of dipeptidyl…”. X-ray diffraction, 5 ligands (NAG, FUL, BMA), 20 pockets (best druggability 0.78). MolNFT v1 #32114 on GenesisL1: 3D structure…
- PDB
- 2BGN
- Type
- protein
- Length
- 4,344 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV; Adenosine deaminase; Tat protein
- EC
- 3.4.14.5, 3.5.4.4
- UniProt
- P27487, P56658, P12506
- Ligands
- NAG, FUL, BMA, MAN, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dipeptidyl peptidase IV (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
| E, F, G, H | Adenosine deaminase (EC 3.5.4.4) | protein | 352 | 50% helix, 14% strand | P56658 |
| W, X, Y, Z | Tat protein | protein | 6 | 0% helix, 0% strand | P12506 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains A, F, B, E, C, G, D, H
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains F, E, G, H
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains F, E, G, H
- ZN · Zinc ion · metal · 4 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.78 | 0.81 | 118 | empty |
| 2 | 82 | 0.77 | 0.98 | 24 | empty |
| 3 | 92 | 0.77 | 0.97 | 24 | empty |
| 4 | 842 | 0.76 | 0.80 | 93 | empty |
| 5 | 721 | 0.75 | 0.80 | 80 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2308 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2306 Ų buried · 39 hydrogen bonds · protein-protein
- A–F · 857 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 856 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 850 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan, 20 disulfide (N-glycosylation, disulfide).
Compared structures
- 2BGN · HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site… · the same entry in another collection · chain Z against Z, 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 P56658
- Every structure of UniProt P12506
- Elsewhere: RCSB PDB 2BGN · PDBe 2BGN · UniProt P27487 · UniProt P56658 · UniProt P12506
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