Research workbench
Crystal structure of the peptidase domain of collagenase T from clostridium tetani complexed with the peptidic inhibitor isoamyl- phosphonyl-gly-pro-ala at 2.05 ångström resolution.
Analyse Crystal structure of the peptidase domain of collagenase T from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AR8
- Type
- protein
- Length
- 786 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase colt; Isoamyl-phosphonyl-gly-pro-ala
- UniProt
- Q899Y1
- Ligands
- IP8, ZN, CA
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase colt | protein | 391 | 49% helix, 17% strand | Q899Y1 |
| B | Collagenase colt | protein | 389 | 49% helix, 17% strand | Q899Y1 |
| C, D | Isoamyl-phosphonyl-gly-pro-ala | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- IP8 · Isopentenyl phosphate · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.76 | 0.84 | 51 | empty |
| 2 | 873 | 0.73 | 0.78 | 80 | empty |
| 3 | 213 | 0.59 | 0.80 | 27 | empty |
| 4 | 133 | 0.59 | 0.84 | 25 | empty |
| 5 | 149 | 0.56 | 0.82 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 594 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 269 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4AR8 · Crystal structure of the peptidase domain of collagenase T from Clostridium tetani… · the same entry in another collection · chain A against A, TM-score 1.00
- Q899Y1 · AlphaFold monomer V2.0 prediction for collagenase colt (Q899Y1) · a predicted model of the same protein · chain A 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 Q899Y1
- Elsewhere: RCSB PDB 4AR8 · PDBe 4AR8 · UniProt Q899Y1
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