Research workbench
Ligand binding domain of P. putida KT2440 polyamine chemorecpetors mcpu in complex putrescine.
Analyse Ligand binding domain of P. putida KT2440 polyamine chemorecpetors mcpu in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F9G
- Type
- protein
- Length
- 1,305 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis protein mcpu
- UniProt
- Q88NI1
- Ligands
- PUT
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Methyl-accepting chemotaxis protein mcpu | protein | 261 | 33% helix, 32% strand | Q88NI1 |
| C | Methyl-accepting chemotaxis protein mcpu | protein | 260 | 32% helix, 32% strand | Q88NI1 |
| D | Methyl-accepting chemotaxis protein mcpu | protein | 262 | 34% helix, 33% strand | Q88NI1 |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 5 copies · chains A, C, D, E
- ACT · Acetate ion · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.69 | 0.79 | 51 | empty |
| 2 | 160 | 0.67 | 0.87 | 21 | empty |
| 3 | 192 | 0.58 | 0.81 | 26 | empty |
| 4 | 291 | 0.56 | 0.76 | 57 | PUT, GOL |
| 5 | 284 | 0.54 | 0.76 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1514 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1402 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 439 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 421 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6F9G · Ligand binding domain of P. putida KT2440 polyamine chemorecpetors McpU in complex… · the same entry in another collection · chain E against E, TM-score 1.00
- Q88NI1 · AlphaFold monomer V2.0 prediction for methyl-accepting chemotaxis protein mcpu (Q88NI1) · a predicted model of the same protein · chain D 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 Q88NI1
- Elsewhere: RCSB PDB 6F9G · PDBe 6F9G · UniProt Q88NI1
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