Research workbench
Human carboxypeptidase A4 in complex with human latexin.
Analyse Human carboxypeptidase A4 in complex with human latexin. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BO9
- Type
- protein
- Length
- 1,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase A4; Human latexin
- UniProt
- Q9UI42, Q9BS40
- Ligands
- VAL, ACN, NAG, ZN
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Carboxypeptidase A4 | protein | 307 | 38% helix, 18% strand | Q9UI42 |
| B, D | Human latexin | protein | 217 | 24% helix, 44% strand | Q9BS40 |
Ligands and binding sites
- VAL · Valine · ligand · 2 copies · chains A, B, C, D
- ACN · Acetone · ligand · chains D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.78 | 0.80 | 83 | MPD |
| 2 | 89 | 0.73 | 0.96 | 18 | MPD |
| 3 | 84 | 0.73 | 0.96 | 18 | MPD |
| 4 | 60 | 0.73 | 0.99 | 25 | VAL |
| 5 | 447 | 0.71 | 0.81 | 43 | MPD |
Interfaces
4 interfaces between chains.
- A–B · 1223 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 290 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 255 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2BO9 · Human carboxypeptidase A4 in complex with human latexin. · the same entry in another collection · chain B against B, TM-score 1.00
- Q9BS40 · AlphaFold monomer V2.0 prediction for latexin (Q9BS40) · a predicted model of the same protein · chain D against A, TM-score 1.00
- Q9UI42 · AlphaFold monomer V2.0 prediction for carboxypeptidase A4 (Q9UI42) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9UI42
- Every structure of UniProt Q9BS40
- Elsewhere: RCSB PDB 2BO9 · PDBe 2BO9 · UniProt Q9UI42 · UniProt Q9BS40
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