Research workbench
Productive complex between mmp-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR
Analyse Productive complex between mmp-12 and synthetic 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
- 2N8R
- Type
- protein
- Length
- 272 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage metalloelastase; Collagen triple helix repeat family protein
- EC
- 3.4.24.65
- UniProt
- P39900
- Ligands
- CA, ZN
- Pockets
- 2 · best druggability 0.45
Structure
solution nmr · 2 distinct chains · 20% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage metalloelastase (EC 3.4.24.65) | protein | 164 | 24% helix, 18% strand | P39900 |
| B, C, D | Collagen triple helix repeat family protein | protein | 36 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.45 | 0.81 | 18 | empty |
| 2 | 72 | 0.32 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1133 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1103 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1062 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 689 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (hydroxylation).
Compared structures
- 2N8R · Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through… · 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
- Every structure of UniProt P39900
- Elsewhere: RCSB PDB 2N8R · PDBe 2N8R · UniProt P39900
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