Research workbench
Structure of the cheb methylsterase from P. atrosepticum SCRI1043
Analyse Structure of the cheb methylsterase from P. atrosepticum SCRI1043 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMZ
- Type
- protein
- Length
- 1,688 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-glutamate METHYLESTERASE/PROTEIN-glutamine glutaminase
- EC
- 3.1.1.61, 3.5.1.44
- UniProt
- Q6D6I7
- Ligands
- NA, SO4
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-glutamate METHYLESTERASE/PROTEIN-glutamine glutaminase (EC 3.1.1.61, 3.5.1.44) | protein | 342 | 40% helix, 23% strand | Q6D6I7 |
| B | Protein-glutamate METHYLESTERASE/PROTEIN-glutamine glutaminase (EC 3.1.1.61, 3.5.1.44) | protein | 341 | 39% helix, 23% strand | Q6D6I7 |
| C | Protein-glutamate METHYLESTERASE/PROTEIN-glutamine glutaminase (EC 3.1.1.61, 3.5.1.44) | protein | 341 | 39% helix, 23% strand | Q6D6I7 |
| D | Protein-glutamate METHYLESTERASE/PROTEIN-glutamine glutaminase (EC 3.1.1.61, 3.5.1.44) | protein | 336 | 39% helix, 24% strand | Q6D6I7 |
| E | Protein-glutamate METHYLESTERASE/PROTEIN-glutamine glutaminase (EC 3.1.1.61, 3.5.1.44) | protein | 328 | 39% helix, 24% strand | Q6D6I7 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · chains E
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.75 | 0.78 | 92 | GOL, NA |
| 2 | 847 | 0.74 | 0.78 | 78 | GOL |
| 3 | 864 | 0.73 | 0.78 | 79 | empty |
| 4 | 348 | 0.66 | 0.80 | 48 | empty |
| 5 | 449 | 0.66 | 0.78 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 887 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 616 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 580 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YMZ · Structure of the CheB methylsterase from P. atrosepticum SCRI1043 · the same entry in another collection · chain E against E, TM-score 1.00
- Q6D6I7 · AlphaFold monomer V2.0 prediction for protein-glutamate METHYLESTERASE/PROTEIN-glutamine… · a predicted model of the same protein · chain E 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 Q6D6I7
- Elsewhere: RCSB PDB 6YMZ · PDBe 6YMZ · UniProt Q6D6I7
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