Research workbench
Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor
Analyse Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XUD
- Type
- protein
- Length
- 335 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
- PB4, ZN, CA
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 169 | 24% helix, 18% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 24% helix, 17% strand | P45452 |
Ligands and binding sites
- PB4 · N,N'-bis(4-fluoro-3-methylbenzyl)pyrimidine-4,6-dicarboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.72 | 0.79 | 78 | PB4 |
| 2 | 231 | 0.62 | 0.81 | 39 | ZN, PB4 |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 1XUD · PDBe 1XUD · UniProt P45452
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