Research workbench
Collagenase-3 (mmp-13) complexed to a sulphone-based hydroxamic acid
Analyse Collagenase-3 (mmp-13) complexed to a sulphone-based hydroxamic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 830C
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mmp-13
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- RS1, ZN, CA
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mmp-13 (EC 3.4.24.-) | protein | 164 | 24% helix, 20% strand | P45452 |
| B | Mmp-13 (EC 3.4.24.-) | protein | 166 | 23% helix, 19% strand | P45452 |
Ligands and binding sites
- RS1 · 4-[4-(4-chloro-phenoxy)-benzenesulfonylmethyl]-tetrahydro-pyran-4-carboxylic acid hydroxyamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- 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
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 | 1064 | 0.74 | 0.77 | 109 | ZN, RS1 |
Interfaces
1 interface between chains.
- A–B · 1249 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 830C · Collagenase-3 (mmp-13) complexed to a sulphone-based hydroxamic acid · 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 P45452
- Elsewhere: RCSB PDB 830C · PDBe 830C · UniProt P45452
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