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The 2.4 ångström crystal structure of KEX2 in complex with a peptidyl- boronic acid inhibitor
Analyse The 2.4 ångström crystal structure of KEX2 in complex with a peptidyl- boronic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OT5
- Type
- protein
- Length
- 958 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kexin; Ac-ala-lys-boroarg N-acetylated boronic acid peptide inhibitor
- EC
- 3.4.21.61
- UniProt
- P13134
- Ligands
- ACE, BOR, NAG, CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kexin (EC 3.4.21.61) | protein | 477 | 22% helix, 27% strand | P13134 |
| C, D | Ac-ala-lys-boroarg N-acetylated boronic acid peptide inhibitor | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- BOR · (1R)-1-amino-4-{[(E)-amino(imino) methyl]amino}butylboronic acid · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.80 | 0.83 | 99 | ACE |
| 2 | 204 | 0.57 | 0.79 | 23 | empty |
| 3 | 197 | 0.56 | 0.79 | 21 | empty |
| 4 | 123 | 0.47 | 0.79 | 17 | empty |
| 5 | 162 | 0.45 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 700 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 227 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 226 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 4 disulfide, 4 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 1OT5 · The 2.4 Angstrom Crystal Structure of Kex2 in complex with a peptidyl-boronic acid… · the same entry in another collection · chain A against A, TM-score 1.00
- P13134 · AlphaFold monomer V2.0 prediction for kexin (P13134) · 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 P13134
- Elsewhere: RCSB PDB 1OT5 · PDBe 1OT5 · UniProt P13134
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