Research workbench
Crystal structure of human mmp-2 catalytic domain in complex with inhibitor
Analyse Crystal structure of human mmp-2 catalytic domain in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XGJ
- Type
- protein
- Length
- 511 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-2; Gzs-asn-asp-ala-leu-H0F
- EC
- 3.4.24.24
- Ligands
- GZS, H0F, CA, ZN
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase-2 (EC 3.4.24.24) | protein | 168 | 23% helix, 19% strand | — |
| B | Matrix metalloproteinase-2 (EC 3.4.24.24) | protein | 165 | 25% helix, 18% strand | — |
| C | Matrix metalloproteinase-2 (EC 3.4.24.24) | protein | 166 | 23% helix, 17% strand | — |
| D, E, F | Gzs-asn-asp-ala-leu-H0F | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- GZS · 4-[(4-phenoxyphenyl)sulfonylamino]butanoic acid · ligand · 3 copies · chains A, D, B, E, C, F
- H0F · 2-[(2~{S})-1-[(2~{S},3~{S})-3-methyl-2-(methylamino) pentanoyl]pyrrolidin-2-yl]ethanamide · ligand · 3 copies · chains A, D, B, C, E, F
- CA · Calcium ion · metal · 9 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.67 | 0.82 | 46 | CA |
| 2 | 450 | 0.60 | 0.75 | 28 | H0F |
| 3 | 168 | 0.60 | 0.83 | 29 | GZS |
| 4 | 148 | 0.58 | 0.83 | 25 | GZS |
| 5 | 126 | 0.58 | 0.84 | 24 | GZS |
Interfaces
5 interfaces between chains.
- A–B · 637 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 355 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 351 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 342 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7XGJ · Crystal structure of human MMP-2 catalytic domain in complex with inhibitor · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 7XGJ · PDBe 7XGJ
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