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Catalytic domain of prommp-2 E404Q mutant
Analyse Catalytic domain of prommp-2 E404Q mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EAK
- Type
- protein
- Length
- 1,693 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 72 kda type IV collagenase; Inhibitor peptide
- EC
- 3.4.24.24
- UniProt
- P08253
- Ligands
- ZN, CA, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 72 kda type IV collagenase (EC 3.4.24.24) | protein | 421 | 19% helix, 18% strand | P08253 |
| B, D | 72 kda type IV collagenase (EC 3.4.24.24) | protein | 419 | 20% helix, 19% strand | P08253 |
| C | 72 kda type IV collagenase (EC 3.4.24.24) | protein | 418 | 17% helix, 17% strand | P08253 |
| P, R | Inhibitor peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D, R, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.82 | 0.83 | 100 | SO4 |
| 2 | 1035 | 0.82 | 0.83 | 90 | SO4 |
| 3 | 857 | 0.77 | 0.81 | 68 | empty |
| 4 | 496 | 0.75 | 0.83 | 56 | empty |
| 5 | 340 | 0.68 | 0.81 | 42 | empty |
Interfaces
7 interfaces between chains.
- B–D · 1025 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1002 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 613 Ų buried · 1 hydrogen bond · protein-protein
- A–P · 512 Ų buried · 8 hydrogen bonds · protein-protein
- D–R · 492 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
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 P08253
- Elsewhere: RCSB PDB 1EAK · PDBe 1EAK · UniProt P08253
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