Research workbench
The crystal structure of the complex of the C-terminal domain of helicobacter pylori motb (residues 125-256) with N-acetylmuramic acid
Analyse The crystal structure of the complex of the C-terminal domain of helicobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CYQ
- Type
- protein
- Length
- 2,123 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemotaxis protein motb
- UniProt
- P56427
- Ligands
- AMU
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, F, A, M | Chemotaxis protein motb | protein | 133 | 44% helix, 16% strand | P56427 |
| D, E, H, I, K, L, O, P | Chemotaxis protein motb | protein | 132 | 45% helix, 17% strand | P56427 |
| G, J, N | Chemotaxis protein motb | protein | 134 | 43% helix, 18% strand | P56427 |
Ligands and binding sites
- AMU · N-acetyl-beta-muramic acid · ligand · 2 copies · chains D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 898 | 0.80 | 0.83 | 99 | empty |
| 2 | 818 | 0.79 | 0.82 | 90 | empty |
| 3 | 793 | 0.78 | 0.82 | 94 | empty |
| 4 | 702 | 0.77 | 0.82 | 78 | empty |
| 5 | 106 | 0.63 | 0.88 | 21 | empty |
Interfaces
30 interfaces between chains.
- G–H · 889 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 868 Ų buried · 15 hydrogen bonds · protein-protein
- F–I · 864 Ų buried · 14 hydrogen bonds · protein-protein
- N–O · 843 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 841 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3CYQ · The crystal structure of the complex of the C-terminal domain of Helicobacter pylori MotB… · the same entry in another collection · chain P against P, 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 P56427
- Elsewhere: RCSB PDB 3CYQ · PDBe 3CYQ · UniProt P56427
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