Research workbench
Crystal structure of human fibrillar procollagen type III C- propeptide trimer
Analyse Crystal structure of human fibrillar procollagen type III C- propeptide trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AE2
- Type
- protein
- Length
- 638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen alpha-1(III) chain
- UniProt
- P02461
- Ligands
- CA, NO3
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen alpha-1(III) chain | protein | 212 | 15% helix, 33% strand | P02461 |
| B | Collagen alpha-1(III) chain | protein | 214 | 14% helix, 33% strand | P02461 |
| C | Collagen alpha-1(III) chain | protein | 212 | 14% helix, 33% strand | P02461 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NO3 · Nitrate ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.77 | 0.79 | 75 | empty |
| 2 | 236 | 0.57 | 0.78 | 45 | NO3 |
| 3 | 85 | 0.53 | 0.85 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 775 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 689 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4AE2 · Crystal structure of Human fibrillar procollagen type III C- propeptide trimer · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 4AE2 · PDBe 4AE2 · UniProt P02461
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