Research workbench
Human collagenase 3 (mmp-13) full form with peptides from pro-domain
Analyse Human collagenase 3 (mmp-13) full form with peptides from pro-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FVL
- Type
- protein
- Length
- 770 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3; Collagenase 3, pro-domain peptide
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- CA, ZN, CL
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Collagenase 3 (EC 3.4.24.-) | protein | 368 | 17% helix, 33% strand | P45452 |
| C | Collagenase 3, pro-domain peptide (EC 3.4.24.-) | protein | 14 | 0% helix, 36% strand | P45452 |
| D | Collagenase 3, pro-domain peptide (EC 3.4.24.-) | protein | 20 | 50% helix, 25% strand | P45452 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 3 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 28 copies · chains A, C, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.67 | 0.88 | 26 | PGO |
| 2 | 129 | 0.59 | 0.84 | 25 | PGO |
| 3 | 60 | 0.50 | 0.86 | 15 | empty |
| 4 | 68 | 0.43 | 0.81 | 13 | empty |
| 5 | 68 | 0.42 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 969 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 951 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 620 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4FVL · Human collagenase 3 (MMP-13) full form with peptides from pro-domain · 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 4FVL · PDBe 4FVL · UniProt P45452
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