MolNFT v1 · #146393 · protein
Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with caesium
6DG3 · Pyridinium-3,5-biscarboxylic acid mononucleotide…: “Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with caesium”. X-ray diffraction, 2 ligands (CS, PO4), 20 pockets (best…
- PDB
- 6DG3
- Type
- protein
- Length
- 2,874 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
- EC
- 2.8.1.-
- UniProt
- F9UST4
- Ligands
- CS, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 12 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 245 | 53% helix, 16% strand | F9UST4 |
| B | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 204 | 48% helix, 17% strand | F9UST4 |
| C | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 246 | 52% helix, 16% strand | F9UST4 |
| D | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 244 | 52% helix, 16% strand | F9UST4 |
| E | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 221 | 53% helix, 16% strand | F9UST4 |
| F | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 247 | 51% helix, 15% strand | F9UST4 |
| G | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 250 | 54% helix, 16% strand | F9UST4 |
| H | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 245 | 53% helix, 15% strand | F9UST4 |
| I | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 247 | 54% helix, 16% strand | F9UST4 |
| J | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 249 | 51% helix, 14% strand | F9UST4 |
| K | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 235 | 53% helix, 14% strand | F9UST4 |
| L | Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase (EC 2.8.1.-) | protein | 241 | 54% helix, 16% strand | F9UST4 |
Ligands and binding sites
- CS · Cesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.83 | 0.95 | 43 | empty |
| 2 | 815 | 0.76 | 0.80 | 98 | CS |
| 3 | 537 | 0.71 | 0.80 | 60 | empty |
| 4 | 653 | 0.71 | 0.79 | 70 | empty |
| 5 | 662 | 0.70 | 0.78 | 62 | empty |
Interfaces
22 interfaces between chains.
- C–H · 848 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 842 Ų buried · 4 hydrogen bonds · protein-protein
- I–K · 837 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 836 Ų buried · 6 hydrogen bonds · protein-protein
- E–J · 836 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6DG3 · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in… · the same entry in another collection · chain L against L, 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 F9UST4
- Elsewhere: RCSB PDB 6DG3 · PDBe 6DG3 · UniProt F9UST4
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