Research workbench
Crystal structure of E.COLI mnmg (gida), a highly-conserved tRNA modifying enzyme
Analyse Crystal structure of E.COLI mnmg (gida), a highly-conserved tRNA modifying… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CES
- Type
- protein
- Length
- 2,073 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida
- UniProt
- P0A6U3
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida | protein | 531 | 38% helix, 21% strand | P0A6U3 |
| B | TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida | protein | 519 | 37% helix, 21% strand | P0A6U3 |
| C | TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida | protein | 516 | 37% helix, 21% strand | P0A6U3 |
| D | TRNA uridine 5-carboxymethylaminomethyl modification enzyme gida | protein | 507 | 37% helix, 20% strand | P0A6U3 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.78 | 0.83 | 83 | empty |
| 2 | 858 | 0.77 | 0.81 | 104 | empty |
| 3 | 585 | 0.76 | 0.83 | 67 | empty |
| 4 | 515 | 0.74 | 0.83 | 62 | empty |
| 5 | 58 | 0.72 | 0.98 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1740 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1564 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 89 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3CES · Crystal Structure of E.coli MnmG (GidA), a Highly-Conserved tRNA Modifying Enzyme · the same entry in another collection · chain D against D, TM-score 1.00
- P0A6U3 · AlphaFold monomer V2.0 prediction for tRNA uridine 5-carboxymethylaminomethyl… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P0A6U3
- Elsewhere: RCSB PDB 3CES · PDBe 3CES · UniProt P0A6U3
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