MolNFT v1 · #135934 · protein
Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with AMP
5UDT · Lactate racemization operon protein lare: “Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with AMP”. X-ray diffraction, 2 ligands (AMP, PO4), 20 pockets (best druggability 0.80).…
- PDB
- 5UDT
- Type
- protein
- Length
- 1,393 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate racemization operon protein lare
- UniProt
- F9UST4
- Ligands
- AMP, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lactate racemization operon protein lare | protein | 256 | 52% helix, 16% strand | F9UST4 |
| B | Lactate racemization operon protein lare | protein | 252 | 52% helix, 18% strand | F9UST4 |
| D | Lactate racemization operon protein lare | protein | 186 | 48% helix, 12% strand | F9UST4 |
| E | Lactate racemization operon protein lare | protein | 244 | 50% helix, 16% strand | F9UST4 |
| F | Lactate racemization operon protein lare | protein | 199 | 48% helix, 16% strand | F9UST4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.80 | 0.96 | 38 | empty |
| 2 | 122 | 0.73 | 0.93 | 31 | empty |
| 3 | 666 | 0.72 | 0.79 | 57 | AMP |
| 4 | 434 | 0.70 | 0.81 | 39 | AMP |
| 5 | 570 | 0.70 | 0.79 | 51 | AMP |
Interfaces
12 interfaces between chains.
- C–E · 844 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 837 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 829 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 458 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5UDT · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in… · the same entry in another collection · chain F against F, TM-score 1.00
- F9UST4 · AlphaFold monomer V2.0 prediction for pyridinium-3,5-bisthiocarboxylic acid… · a predicted model of the same protein · chain E 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 F9UST4
- Elsewhere: RCSB PDB 5UDT · PDBe 5UDT · UniProt F9UST4
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