Research workbench
Co-crystal structure of dppiv with a chemibody inhibitor
Analyse Co-crystal structure of dppiv with a chemibody inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VTA
- Type
- protein
- Length
- 4,161 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4; Fab light chain; Fab heavy chain
- EC
- 3.4.14.5
- UniProt
- P14740
- Ligands
- 9K4, NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 10 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 38% strand | P14740 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 718 | 18% helix, 37% strand | P14740 |
| D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 18% helix, 36% strand | P14740 |
| L | Fab light chain | protein | 208 | 6% helix, 47% strand | — |
| E | Fab light chain | protein | 204 | 7% helix, 49% strand | — |
| H, F | Fab heavy chain | protein | 217 | 7% helix, 55% strand | — |
| G | Fab light chain | protein | 100 | 3% helix, 42% strand | — |
| I | Fab heavy chain | protein | 115 | 5% helix, 41% strand | — |
| J | Fab light chain | protein | 89 | 0% helix, 52% strand | — |
| K | Fab heavy chain | protein | 110 | 0% helix, 42% strand | — |
Ligands and binding sites
- 9K4 · 2-{4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl) butanoyl]piperazin-1-yl}-N-(22-oxo-3,6,9,12,15,18-hexaoxa-21-azatricosan-1-yl)acetamide · ligand · 4 copies · chains A, B, G, C, D, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, C, E, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, D
- PG4 · Tetraethylene glycol · additive · chains A, B
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 | 999 | 0.73 | 0.77 | 103 | empty |
| 2 | 1154 | 0.73 | 0.76 | 101 | empty |
| 3 | 989 | 0.73 | 0.76 | 89 | PEG |
| 4 | 53 | 0.73 | 0.99 | 18 | EDO |
| 5 | 897 | 0.71 | 0.76 | 86 | EDO |
Interfaces
21 interfaces between chains.
- A–B · 2310 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2281 Ų buried · 40 hydrogen bonds · protein-protein
- L–H · 1833 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1806 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 858 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 5VTA · Co-Crystal Structure of DPPIV with a Chemibody Inhibitor · the same entry in another collection · chain K against K, 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 P14740
- Elsewhere: RCSB PDB 5VTA · PDBe 5VTA · UniProt P14740
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