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Crystal structure of bacterial cysteine methyltransferase effector nlee
Analyse Crystal structure of bacterial cysteine methyltransferase effector nlee in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R29
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q7DBA6
- Ligands
- SAM
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 199 | 53% helix, 13% strand | Q7DBA6 |
| B | Uncharacterized protein | protein | 203 | 53% helix, 13% strand | Q7DBA6 |
| C | Uncharacterized protein | protein | 203 | 51% helix, 13% strand | Q7DBA6 |
| D | Uncharacterized protein | protein | 199 | 52% helix, 13% strand | Q7DBA6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D
- CIT · Citric acid · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.69 | 0.75 | 87 | SAM, GOL |
| 2 | 677 | 0.66 | 0.75 | 56 | SAM, CIT, GOL |
| 3 | 292 | 0.56 | 0.76 | 36 | SAM, GOL |
| 4 | 256 | 0.55 | 0.76 | 30 | SAM, CIT |
| 5 | 132 | 0.46 | 0.77 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–D · 921 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 428 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 382 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 354 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4R29 · Crystal structure of bacterial cysteine methyltransferase effector NleE · the same entry in another collection · chain D against D, TM-score 1.00
- Q7DBA6 · AlphaFold monomer V2.0 prediction for cysteine S-methyltransferase nlee (Q7DBA6) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q7DBA6
- Elsewhere: RCSB PDB 4R29 · PDBe 4R29 · UniProt Q7DBA6
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