MolNFT v1 · #148533 · protein
Ligand binding domain of P. putida KT2440 polyamine chemorecpetors mcpu in complex putrescine.
6F9G · Methyl-accepting chemotaxis protein mcpu: “Ligand binding domain of P. putida KT2440 polyamine chemorecpetors mcpu in complex putrescine.”. X-ray diffraction, 1 ligand (PUT), 20 pockets (best druggability 0.69). MolNFT v1 #148533 on…
- 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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