Research workbench
Crystal structure of N-terminal domain (2-550) of E.COLI mnmg
Analyse Crystal structure of N-terminal domain (2-550) of E.COLI mnmg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G05
- Type
- protein
- Length
- 1,051 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg
- UniProt
- Q8XAY0
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg | protein | 527 | 34% helix, 20% strand | Q8XAY0 |
| B | TRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmg | protein | 524 | 34% helix, 18% strand | Q8XAY0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.86 | 0.87 | 128 | SO4 |
| 2 | 230 | 0.73 | 0.88 | 32 | empty |
| 3 | 53 | 0.72 | 0.99 | 16 | empty |
| 4 | 240 | 0.72 | 0.87 | 36 | empty |
| 5 | 58 | 0.70 | 0.97 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1549 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3G05 · Crystal structure of N-terminal domain (2-550) of E.coli MnmG · the same entry in another collection · chain A against A, TM-score 1.00
- Q8XAY0 · 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 Q8XAY0
- Elsewhere: RCSB PDB 3G05 · PDBe 3G05 · UniProt Q8XAY0
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