Research workbench
Crystal structure of a clostripain (PARMER_00083) from parabacteroides merdae atcc 43184 in complex with peptide inhibitor ac-vltk-aomk
Analyse Crystal structure of a clostripain (PARMER_00083) from parabacteroides merdae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YEC
- Type
- protein
- Length
- 357 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clostripain family; Peptide inhibitor ac-vltk-aomk
- UniProt
- A7A9N3
- Ligands
- ACE, CKC
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clostripain family | protein | 126 | 29% helix, 35% strand | A7A9N3 |
| B | Clostripain family | protein | 228 | 41% helix, 21% strand | A7A9N3 |
| C | Peptide inhibitor ac-vltk-aomk | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, C
- CKC · (3S)-3,7-diaminoheptan-2-one · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.54 | 0.81 | 32 | CKC |
Interfaces
3 interfaces between chains.
- A–B · 2678 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4YEC · Crystal structure of a clostripain (PARMER_00083) from Parabacteroides merdae ATCC 43184… · the same entry in another collection · 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 A7A9N3
- Elsewhere: RCSB PDB 4YEC · PDBe 4YEC · UniProt A7A9N3
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