Research workbench
Crystal structure of mmp-13 in complex with sc-78080
Analyse Crystal structure of mmp-13 in complex with sc-78080 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KRY
- Type
- protein
- Length
- 654 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
- 3KR, ZN, CA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Collagenase 3 (EC 3.4.24.-) | protein | 164 | 24% helix, 19% strand | P45452 |
| D | Collagenase 3 (EC 3.4.24.-) | protein | 162 | 25% helix, 19% strand | P45452 |
Ligands and binding sites
- 3KR · 1-(2-methoxyethyl)-N-oxo-4-({4-[4-(trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.74 | 0.77 | 93 | ZN, 3KR |
| 2 | 966 | 0.74 | 0.77 | 68 | empty |
| 3 | 326 | 0.70 | 0.84 | 48 | empty |
| 4 | 166 | 0.56 | 0.81 | 26 | ZN, 3KR |
| 5 | 170 | 0.56 | 0.80 | 33 | ZN, 3KR |
Interfaces
5 interfaces between chains.
- A–D · 1016 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 725 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 151 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 140 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KRY · Crystal structure of MMP-13 in complex with SC-78080 · 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 3KRY · PDBe 3KRY · UniProt P45452
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