Research workbench
Crystal structure of mgs-MT1, an ALPHA/BETA hydrolase enzyme from a lake matapan deep-sea metagenome library
Analyse Crystal structure of mgs-MT1, an ALPHA/BETA hydrolase enzyme from a lake… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q3O
- Type
- protein
- Length
- 2,530 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mgs-MT1
- Ligands
- CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mgs-MT1 | protein | 317 | 45% helix, 15% strand | — |
| C, D, E, F, G, H | Mgs-MT1 | protein | 316 | 45% helix, 15% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 10 copies · chains A, B, C, F, E, H, D, G
- GOL · Glycerol · additive · 17 copies · chains A, E, B, C, D, F, G
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 10 copies · chains A, B, E, C, F, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.82 | 0.87 | 49 | GOL, CL |
| 2 | 915 | 0.79 | 0.81 | 62 | GOL |
| 3 | 774 | 0.76 | 0.80 | 63 | CL |
| 4 | 846 | 0.75 | 0.79 | 55 | MES |
| 5 | 482 | 0.73 | 0.82 | 40 | CL |
Interfaces
9 interfaces between chains.
- A–B · 1432 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 1401 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 1395 Ų buried · 26 hydrogen bonds · protein-protein
- D–G · 1382 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 726 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4Q3O · Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from a Lake Matapan deep-sea… · 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 4Q3O · PDBe 4Q3O
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.