Research workbench
Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with cobalt
Analyse Lare, a sulfur transferase involved in synthesis of the cofactor for lactate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UTP
- Type
- protein
- Length
- 1,451 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent sacrificial sulfur transferase lare
- UniProt
- A0A0G9FES3
- Ligands
- CO, SO4, PO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent sacrificial sulfur transferase lare | protein | 243 | 53% helix, 16% strand | A0A0G9FES3 |
| B | ATP-dependent sacrificial sulfur transferase lare | protein | 245 | 48% helix, 16% strand | A0A0G9FES3 |
| C | ATP-dependent sacrificial sulfur transferase lare | protein | 249 | 51% helix, 16% strand | A0A0G9FES3 |
| D | ATP-dependent sacrificial sulfur transferase lare | protein | 239 | 49% helix, 15% strand | A0A0G9FES3 |
| E | ATP-dependent sacrificial sulfur transferase lare | protein | 225 | 50% helix, 15% strand | A0A0G9FES3 |
| F | ATP-dependent sacrificial sulfur transferase lare | protein | 250 | 50% helix, 15% strand | A0A0G9FES3 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, F
- 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
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.78 | 0.97 | 40 | empty |
| 2 | 426 | 0.71 | 0.82 | 41 | SO4 |
| 3 | 586 | 0.69 | 0.78 | 67 | SO4 |
| 4 | 511 | 0.68 | 0.78 | 52 | SO4 |
| 5 | 423 | 0.63 | 0.77 | 54 | PO4, SO4 |
Interfaces
12 interfaces between chains.
- B–D · 885 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 871 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 816 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 599 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 598 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6UTP · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in… · 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 A0A0G9FES3
- Elsewhere: RCSB PDB 6UTP · PDBe 6UTP · UniProt A0A0G9FES3
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