MolNFT v1 · #156047 · protein
Crystal structure of the ternary complex of agre with ornithine and NAD+
6LRG · ALR4995 protein: “Crystal structure of the ternary complex of agre with ornithine and NAD+”. X-ray diffraction, 2 ligands (ORN, NAD), 17 pockets (best druggability 0.75). MolNFT v1 #156047 on GenesisL1: 3D structure, binding sites…
- PDB
- 6LRG
- Type
- protein
- Length
- 1,359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALR4995 protein
- UniProt
- Q8YMD9
- Ligands
- ORN, NAD
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALR4995 protein | protein | 678 | 36% helix, 24% strand | Q8YMD9 |
| B | ALR4995 protein | protein | 681 | 37% helix, 23% strand | Q8YMD9 |
Ligands and binding sites
- ORN · L-ornithine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.75 | 0.98 | 20 | empty |
| 2 | 79 | 0.75 | 0.98 | 24 | empty |
| 3 | 538 | 0.75 | 0.82 | 45 | empty |
| 4 | 89 | 0.69 | 0.93 | 24 | empty |
| 5 | 630 | 0.68 | 0.77 | 61 | empty |
Interfaces
1 interface between chains.
- A–B · 1169 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6LRG · Crystal Structure of the Ternary Complex of AgrE with Ornithine and NAD+ · 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 Q8YMD9
- Elsewhere: RCSB PDB 6LRG · PDBe 6LRG · UniProt Q8YMD9
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