Research workbench
Crystal structure of the metalloproteinase enhancer pcpe-1 bound to the procollagen C propeptide trimer (short)
Analyse Crystal structure of the metalloproteinase enhancer pcpe-1 bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FZV
- Type
- protein
- Length
- 949 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-1(III) chain; Procollagen C-endopeptidase enhancer 1
- UniProt
- P02461, Q15113
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen alpha-1(III) chain | protein | 241 | 20% helix, 28% strand | P02461 |
| B | Collagen alpha-1(III) chain | protein | 239 | 20% helix, 28% strand | P02461 |
| C | Collagen alpha-1(III) chain | protein | 233 | 19% helix, 28% strand | P02461 |
| D | Procollagen C-endopeptidase enhancer 1 | protein | 236 | 0% helix, 44% strand | Q15113 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
- FLC · Citrate anion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.85 | 0.90 | 62 | empty |
| 2 | 1068 | 0.81 | 0.82 | 101 | empty |
| 3 | 936 | 0.75 | 0.79 | 86 | empty |
| 4 | 57 | 0.51 | 0.87 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1166 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 968 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 558 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 422 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6FZV · Crystal structure of the metalloproteinase enhancer PCPE-1 bound to the procollagen C… · the same entry in another collection · chain D against D, TM-score 1.00
- P02461 · AlphaFold monomer V2.0 prediction for collagen alpha-1(III) chain (P02461) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15113 · AlphaFold monomer V2.0 prediction for procollagen C-endopeptidase enhancer 1 (Q15113) · a predicted model of the same protein · chain D against A, TM-score 0.75
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 P02461
- Every structure of UniProt Q15113
- Elsewhere: RCSB PDB 6FZV · PDBe 6FZV · UniProt P02461 · UniProt Q15113
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