Research workbench
Crystal structure of mgs-M4, an aldo-keto reductase enzyme from a medee basin deep-sea metagenome library
Analyse Crystal structure of mgs-M4, an aldo-keto reductase enzyme from a medee basin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q3M
- Type
- protein
- Length
- 1,630 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mgs-M4
- Ligands
- NA, SO4
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Mgs-M4 | protein | 273 | 45% helix, 16% strand | — |
| B | Mgs-M4 | protein | 271 | 45% helix, 16% strand | — |
| E | Mgs-M4 | protein | 272 | 46% helix, 14% strand | — |
| F | Mgs-M4 | protein | 268 | 44% helix, 15% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.74 | 0.77 | 107 | SO4 |
| 2 | 474 | 0.65 | 0.78 | 35 | empty |
| 3 | 507 | 0.61 | 0.75 | 56 | empty |
| 4 | 361 | 0.55 | 0.74 | 36 | empty |
| 5 | 235 | 0.54 | 0.77 | 29 | SO4 |
Interfaces
8 interfaces between chains.
- E–F · 944 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 932 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 354 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 303 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4Q3M · Crystal structure of MGS-M4, an aldo-keto reductase enzyme from a Medee basin deep-sea… · the same entry in another collection · chain B against B, 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 4Q3M · PDBe 4Q3M
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