Research workbench
X-ray structure of mmp-13 in complex with 4-(1,2,3-thiadiazol-4-yl) pyridine
Analyse X-ray structure of mmp-13 in complex with 4-(1,2,3-thiadiazol-4-yl) pyridine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JU8
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- 9DY, 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 | Collagenase 3 (EC 3.4.24.-) | protein | 167 | 24% helix, 19% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 24% helix, 19% strand | P45452 |
Ligands and binding sites
- 9DY · 4-(1,2,3-thiadiazol-4-yl)pyridine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 11 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · 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 | 979 | 0.74 | 0.77 | 99 | ZN, 9DY, PGE, FMT, PG4 |
Interfaces
1 interface between chains.
- A–B · 1233 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7JU8 · X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine · 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 7JU8 · PDBe 7JU8 · UniProt P45452
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