Research workbench
Crystal structure of the metalloproteinase enhancer pcpe-1 bound to the procollagen C propeptide trimer (long)
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
- 6FZW
- Type
- protein
- Length
- 886 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
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen alpha-1(III) chain | protein | 237 | 20% helix, 29% strand | P02461 |
| B | Collagen alpha-1(III) chain | protein | 237 | 21% helix, 29% strand | P02461 |
| C | Collagen alpha-1(III) chain | protein | 232 | 19% helix, 29% strand | P02461 |
| D | Procollagen C-endopeptidase enhancer 1 | protein | 180 | 0% helix, 37% strand | Q15113 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.85 | 0.92 | 61 | empty |
| 2 | 1179 | 0.73 | 0.77 | 89 | FLC |
| 3 | 517 | 0.69 | 0.79 | 54 | empty |
| 4 | 399 | 0.68 | 0.80 | 40 | empty |
| 5 | 59 | 0.42 | 0.82 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1108 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1086 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 970 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 541 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 433 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6FZW · 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 0.82
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 6FZW · PDBe 6FZW · UniProt P02461 · UniProt Q15113
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