Research workbench
X-ray structure of human prommp-1: new insights into collagenase action
Analyse X-ray structure of human prommp-1: new insights into collagenase action in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SU3
- Type
- protein
- Length
- 831 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interstitial collagenase
- EC
- 3.4.24.7
- UniProt
- P03956
- Ligands
- CA, ZN, NA, SO4, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interstitial collagenase (EC 3.4.24.7) | protein | 415 | 20% helix, 27% strand | P03956 |
| B | Interstitial collagenase (EC 3.4.24.7) | protein | 416 | 20% helix, 27% strand | P03956 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.69 | 0.82 | 49 | empty |
| 2 | 369 | 0.63 | 0.78 | 42 | empty |
| 3 | 76 | 0.40 | 0.79 | 23 | empty |
| 4 | 51 | 0.39 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 126 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1SU3 · X-ray structure of human proMMP-1: New insights into collagenase action · the same entry in another collection · chain A against A, TM-score 1.00
- P03956 · AlphaFold monomer V2.0 prediction for interstitial collagenase (P03956) · a predicted model of the same protein · chain B 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 P03956
- Elsewhere: RCSB PDB 1SU3 · PDBe 1SU3 · UniProt P03956
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