Research workbench
Crystal structure of mmp-1(E200A) in complex with a triple- helical collagen peptide
Analyse Crystal structure of mmp-1(E200A) in complex with a triple- helical collagen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AUO
- Type
- protein
- Length
- 947 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interstitial collagenase; Triple-helical collagen peptide
- EC
- 3.4.24.7
- UniProt
- P03956
- Ligands
- CA, ZN
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Interstitial collagenase (EC 3.4.24.7) | protein | 367 | 17% helix, 30% strand | P03956 |
| C | Triple-helical collagen peptide | protein | 39 | 0% helix, 0% strand | — |
| D, F, G | Triple-helical collagen peptide | protein | 36 | 0% helix, 0% strand | — |
| E, H | Triple-helical collagen peptide | protein | 33 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.74 | 0.77 | 116 | empty |
| 2 | 50 | 0.70 | 0.99 | 21 | empty |
| 3 | 54 | 0.69 | 0.97 | 20 | empty |
| 4 | 93 | 0.69 | 0.93 | 22 | empty |
| 5 | 67 | 0.63 | 0.92 | 14 | empty |
Interfaces
19 interfaces between chains.
- C–D · 1351 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1271 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1111 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1104 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 1095 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified, 2 disulfide (hydroxylation, disulfide).
Compared structures
- 4AUO · Crystal structure of MMP-1(E200A) in complex with a triple-helical collagen peptide · the same entry in another collection · chain H against H, TM-score 1.00
- P03956 · AlphaFold monomer V2.0 prediction for interstitial collagenase (P03956) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 4AUO · PDBe 4AUO · UniProt P03956
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