MolNFT v1 · #182173 · protein
Larb, a CARBOXYLASE/HYDROLASE involved in synthesis of the cofactor for lactate racemase, in complex with NAD
7MJ1 · Pyridinium-3,5-biscarboxylic acid mononucleotide synthase: “Larb, a CARBOXYLASE/HYDROLASE involved in synthesis of the cofactor for lactate racemase, in complex with NAD”. X-ray diffraction, 3 ligands (NAD, NAI, MG), 15 pockets…
- PDB
- 7MJ1
- Type
- protein
- Length
- 1,217 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridinium-3,5-biscarboxylic acid mononucleotide synthase
- EC
- 2.5.1.143
- UniProt
- F9UST0
- Ligands
- NAD, NAI, MG
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyridinium-3,5-biscarboxylic acid mononucleotide synthase (EC 2.5.1.143) | protein | 201 | 35% helix, 19% strand | F9UST0 |
| C | Pyridinium-3,5-biscarboxylic acid mononucleotide synthase (EC 2.5.1.143) | protein | 200 | 39% helix, 19% strand | F9UST0 |
| E | Pyridinium-3,5-biscarboxylic acid mononucleotide synthase (EC 2.5.1.143) | protein | 211 | 35% helix, 19% strand | F9UST0 |
| F | Pyridinium-3,5-biscarboxylic acid mononucleotide synthase (EC 2.5.1.143) | protein | 201 | 36% helix, 19% strand | F9UST0 |
| B | Pyridinium-3,5-biscarboxylic acid mononucleotide synthase (EC 2.5.1.143) | protein | 203 | 33% helix, 20% strand | F9UST0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains C
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.67 | 0.86 | 29 | empty |
| 2 | 100 | 0.62 | 0.88 | 24 | empty |
| 3 | 81 | 0.48 | 0.82 | 28 | empty |
| 4 | 186 | 0.48 | 0.75 | 23 | empty |
| 5 | 138 | 0.47 | 0.78 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1149 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1043 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 894 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 363 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7MJ1 · LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase… · the same entry in another collection · chain B against B, TM-score 1.00
- F9UST0 · AlphaFold monomer V2.0 prediction for pyridinium-3,5-biscarboxylic acid mononucleotide… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 F9UST0
- Elsewhere: RCSB PDB 7MJ1 · PDBe 7MJ1 · UniProt F9UST0
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