MolNFT v1 · #92202 · protein
Human collagenase 3 (mmp-13) full form with peptides from pro-domain
4G0D: “Human collagenase 3 (mmp-13) full form with peptides from pro-domain”. X-ray diffraction, 3 ligands (CA, ZN, CL), 20 pockets (best druggability 0.77). MolNFT v1 #92202 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4G0D
- Type
- protein
- Length
- 1,563 residues
- Chains
- 8
- 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
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Collagenase 3 (EC 3.4.24.-) | protein | 368 | 14% helix, 32% strand | P45452 |
| W | Collagenase 3, pro-domain peptide | protein | 19 | 21% helix, 26% strand | P45452 |
| X | Collagenase 3, pro-domain peptide | protein | 26 | 38% helix, 19% strand | P45452 |
| Y, Z | Collagenase 3, pro-domain peptide | protein | 23 | 30% helix, 22% strand | P45452 |
Ligands and binding sites
- CA · Calcium ion · metal · 23 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, W, B, X, C, Y, D, Z
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, Y, Z
- PGO · S-1,2-propanediol · additive · 38 copies · chains A, C, Y, B, W, D
- GOL · Glycerol · additive · 5 copies · chains B, A, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.77 | 0.83 | 63 | CA, GOL |
| 2 | 576 | 0.75 | 0.82 | 76 | PGO |
| 3 | 614 | 0.74 | 0.81 | 77 | PGO |
| 4 | 115 | 0.72 | 0.93 | 24 | PGO |
| 5 | 166 | 0.64 | 0.85 | 32 | PGO |
Interfaces
14 interfaces between chains.
- A–C · 1109 Ų buried · 14 hydrogen bonds · protein-protein
- A–W · 1071 Ų buried · 16 hydrogen bonds · protein-protein
- C–Y · 1059 Ų buried · 13 hydrogen bonds · protein-protein
- B–X · 1041 Ų buried · 14 hydrogen bonds · protein-protein
- D–Z · 1041 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4G0D · 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 4G0D · PDBe 4G0D · UniProt P45452
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