Research workbench
Flexibility and variability of timp binding: X-ray structure of the complex between collagenase-3/MMP-13 and timp-2
Analyse Flexibility and variability of timp binding: X-ray structure of the complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E2D
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metallopeptidase 13; Metalloproteinase inhibitor 2
- EC
- 3.4.24.-
- UniProt
- P45452, P16368
- Ligands
- ZN, CA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metallopeptidase 13 (EC 3.4.24.-) | protein | 165 | 24% helix, 19% strand | P45452 |
| C | Metalloproteinase inhibitor 2 | protein | 180 | 18% helix, 38% strand | P16368 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.64 | 0.78 | 59 | empty |
| 2 | 395 | 0.63 | 0.77 | 38 | empty |
| 3 | 171 | 0.59 | 0.82 | 37 | empty |
| 4 | 263 | 0.57 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–C · 1265 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2E2D · Flexibility and variability of TIMP binding: X-ray structure of the complex between… · the same entry in another collection · chain A against A, TM-score 1.00
- P16368 · AlphaFold monomer V2.0 prediction for metalloproteinase inhibitor 2 (P16368) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P45452
- Every structure of UniProt P16368
- Elsewhere: RCSB PDB 2E2D · PDBe 2E2D · UniProt P45452 · UniProt P16368
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