Research workbench
Crystal structure of the catalytic domain of mmp-13 complexed with way-033
Analyse Crystal structure of the catalytic domain of mmp-13 complexed with way-033 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZTQ
- Type
- protein
- Length
- 631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- 033, CA, ZN
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 162 | 25% helix, 18% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 160 | 24% helix, 19% strand | P45452 |
| C | Collagenase 3 (EC 3.4.24.-) | protein | 153 | 26% helix, 20% strand | P45452 |
| D | Collagenase 3 (EC 3.4.24.-) | protein | 156 | 25% helix, 21% strand | P45452 |
Ligands and binding sites
- 033 · N-({4'-[(1-benzofuran-2-ylcarbonyl)amino]-1,1'-biphenyl-4-yl}sulfonyl)-L-valine · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.75 | 0.79 | 60 | empty |
| 2 | 348 | 0.73 | 0.85 | 44 | empty |
| 3 | 316 | 0.71 | 0.84 | 50 | empty |
| 4 | 166 | 0.55 | 0.80 | 25 | ZN, 033 |
| 5 | 170 | 0.52 | 0.78 | 32 | 033 |
Interfaces
4 interfaces between chains.
- A–D · 757 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 755 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 202 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 178 Ų buried · 2 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 1ZTQ · PDBe 1ZTQ · UniProt P45452
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.