Research workbench
The 1.9 a structure of KEX2 in complex with an ac-R-E-R-K-chloromethyl ketone inhibitor.
Analyse The 1.9 a structure of KEX2 in complex with an ac-R-E-R-K-chloromethyl ketone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ID4
- Type
- protein
- Length
- 967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kexin; Ac-rerk-cmk inhibitor
- EC
- 3.4.21.61
- UniProt
- P13134
- Ligands
- ACE, NAG, NDG, CA, NA, 0QE
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kexin (EC 3.4.21.61) | protein | 480 | 23% helix, 28% strand | P13134 |
| B | Kexin (EC 3.4.21.61) | protein | 479 | 23% helix, 29% strand | P13134 |
| C, D | Ac-rerk-cmk inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- 0QE · Chloromethane · ion · 2 copies · chains A, C, B, D
- MLA · Malonic acid · additive · 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 | 882 | 0.80 | 0.83 | 110 | 0QE, MLA |
| 2 | 198 | 0.55 | 0.79 | 23 | empty |
| 3 | 204 | 0.55 | 0.79 | 25 | empty |
| 4 | 143 | 0.45 | 0.76 | 22 | empty |
| 5 | 79 | 0.42 | 0.80 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 713 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 549 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 538 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan, 4 modified, 2 covalent (disulfide, N-glycosylation, covalent ligand, nonstandard, oxidation).
Compared structures
- 2ID4 · The 1.9 A structure of Kex2 in complex with an Ac-R-E-R-K-chloromethyl ketone inhibitor. · 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 2ID4 · PDBe 2ID4 · UniProt P13134
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