Research workbench
Crystal structure of a methyltransferase (NP_951602.1) from geobacter sulfurreducens at 1.90 a resolution
Analyse Crystal structure of a methyltransferase (NP_951602.1) from geobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C3P
- Type
- protein
- Length
- 583 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- UniProt
- Q74FR2
- Ligands
- CL
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase | protein | 198 | 43% helix, 23% strand | Q74FR2 |
| B | Methyltransferase | protein | 190 | 45% helix, 24% strand | Q74FR2 |
| C | Methyltransferase | protein | 195 | 45% helix, 23% strand | Q74FR2 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.60 | 0.80 | 30 | EDO, PEG |
| 2 | 127 | 0.54 | 0.82 | 30 | EDO |
| 3 | 134 | 0.51 | 0.80 | 29 | EDO |
| 4 | 103 | 0.46 | 0.80 | 28 | empty |
| 5 | 149 | 0.43 | 0.75 | 26 | PEG, EDO |
Interfaces
3 interfaces between chains.
- A–B · 1840 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 265 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 113 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3C3P · Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at… · 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 Q74FR2
- Elsewhere: RCSB PDB 3C3P · PDBe 3C3P · UniProt Q74FR2
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