MolNFT v1 · #15335 · protein
Human dipeptidyl peptidase IV/CD26 in complex with an inhibitor
1N1M · Dipeptidyl peptidase IV soluble form: “Human dipeptidyl peptidase IV/CD26 in complex with an inhibitor”. X-ray diffraction, 7 ligands (A3M, NAG, NDG), 15 pockets (best druggability 0.74). MolNFT v1 #15335 on GenesisL1: 3D structure…
- PDB
- 1N1M
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV soluble form
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- A3M, NAG, NDG, FUC, BMA, MAN, HG
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase IV soluble form (EC 3.4.14.5) | protein | 726 | 18% helix, 37% strand | P27487 |
| B | Dipeptidyl peptidase IV soluble form (EC 3.4.14.5) | protein | 728 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- A3M · 2-amino-3-methyl-1-pyrrolidin-1-yl-butan-1-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- HG · Mercury (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.74 | 0.99 | 23 | empty |
| 2 | 892 | 0.71 | 0.76 | 117 | HG, A3M |
| 3 | 528 | 0.66 | 0.77 | 62 | A3M |
| 4 | 463 | 0.59 | 0.74 | 68 | empty |
| 5 | 284 | 0.54 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2308 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 1N1M · PDBe 1N1M · UniProt P27487
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