MolNFT v1 · #152650 · protein
The ligand binding domain of MLP24 with arginine
6IOT · Methyl-accepting chemotaxis protein: “The ligand binding domain of MLP24 with arginine”. X-ray diffraction, 2 ligands (ARG, CA), 14 pockets (best druggability 0.76). MolNFT v1 #152650 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6IOT
- Type
- protein
- Length
- 959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis protein
- UniProt
- A0A0H6VSA0
- Ligands
- ARG, CA
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-accepting chemotaxis protein | protein | 238 | 37% helix, 30% strand | A0A0H6VSA0 |
| B | Methyl-accepting chemotaxis protein | protein | 239 | 35% helix, 29% strand | A0A0H6VSA0 |
| C | Methyl-accepting chemotaxis protein | protein | 241 | 38% helix, 28% strand | A0A0H6VSA0 |
| D | Methyl-accepting chemotaxis protein | protein | 241 | 36% helix, 28% strand | A0A0H6VSA0 |
Ligands and binding sites
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.76 | 0.98 | 21 | empty |
| 2 | 68 | 0.74 | 0.98 | 20 | empty |
| 3 | 591 | 0.64 | 0.75 | 60 | empty |
| 4 | 54 | 0.61 | 0.92 | 16 | ARG |
| 5 | 325 | 0.56 | 0.75 | 35 | empty |
Interfaces
4 interfaces between chains.
- C–D · 955 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 817 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 664 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6IOT · The ligand binding domain of Mlp24 with arginine · the same entry in another collection · chain A 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 A0A0H6VSA0
- Elsewhere: RCSB PDB 6IOT · PDBe 6IOT · UniProt A0A0H6VSA0
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