Research workbench
Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor
Analyse Crystal structure analysis of the MMP13 catalytic domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OW9
- 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
- SP6, HAE, CA, ZN, SO4
- Pockets
- 2 · best druggability 0.73
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 | 23% helix, 19% strand | P45452 |
Ligands and binding sites
- SP6 · Benzyl 6-benzyl-5,7-dioxo-6,7-dihydro-5H-[1,3]thiazolo[3,2-c]pyrimidine-2-carboxylate · ligand · 2 copies · chains A, B
- HAE · Acetohydroxamic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 719 | 0.73 | 0.79 | 75 | ZN, SP6, HAE |
| 2 | 252 | 0.63 | 0.81 | 43 | SP6, HAE |
Interfaces
1 interface between chains.
- A–B · 1224 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2OW9 · Crystal structure analysis of the MMP13 catalytic domain in complex with specific… · 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 2OW9 · PDBe 2OW9 · UniProt P45452
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