Research workbench
Crystal structure of the stromelysin-3 (mmp-11) catalytic domain complexed with a phosphinic inhibitor
Analyse Crystal structure of the stromelysin-3 (mmp-11) catalytic domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HV5
- Type
- protein
- Length
- 977 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromelysin 3
- EC
- 3.4.24.-
- UniProt
- Q02853
- Ligands
- CPS, RXP, ZN, CA
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Stromelysin 3 (EC 3.4.24.-) | protein | 162 | 23% helix, 24% strand | Q02853 |
| B | Stromelysin 3 (EC 3.4.24.-) | protein | 164 | 24% helix, 24% strand | Q02853 |
| E | Stromelysin 3 (EC 3.4.24.-) | protein | 165 | 24% helix, 23% strand | Q02853 |
Ligands and binding sites
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 12 copies · chains A, E, B, C, D, F
- RXP · 1-benzyloxycarbonylamino-2-phenyl-ethyl)-{2-[1-carbamoyl-2-(1H-indol-3-yl)-ethylcarbamoyl]-5-phenyl-pentyl}-phosphinic acid · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.68 | 0.79 | 64 | RXP |
| 2 | 654 | 0.67 | 0.76 | 44 | CPS |
| 3 | 547 | 0.65 | 0.76 | 39 | CPS |
| 4 | 136 | 0.60 | 0.85 | 26 | ZN, RXP |
| 5 | 114 | 0.57 | 0.84 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 967 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 967 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 417 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 266 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1HV5 · Crystal structure of the stromelysin-3 (mmp-11) catalytic domain complexed with a… · the same entry in another collection · chain F against F, TM-score 1.00
- Q02853 · AlphaFold monomer V2.0 prediction for stromelysin-3 (Q02853) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q02853
- Elsewhere: RCSB PDB 1HV5 · PDBe 1HV5 · UniProt Q02853
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