MolNFT v1 · #59621 · protein
Crystal structure of 2-phospho-(S)-lactate transferase from methanosarcina mazei in complex with fo and phosphate. northeast structural genomics consortium target MAR46
3C3D · 2-phospho-L-lactate transferase: “Crystal structure of 2-phospho-(S)-lactate transferase from methanosarcina mazei in complex with fo and…”. X-ray diffraction, 2 ligands (FO1, PO4), 11 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 3C3D
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-phospho-L-lactate transferase
- EC
- 2.7.8.-
- UniProt
- Q8PVT6
- Ligands
- FO1, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-phospho-L-lactate transferase (EC 2.7.8.-) | protein | 306 | 41% helix, 19% strand | Q8PVT6 |
Ligands and binding sites
- FO1 · 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.78 | 0.86 | 48 | FO1, PO4 |
| 2 | 427 | 0.77 | 0.85 | 51 | FO1, PO4 |
| 3 | 404 | 0.77 | 0.86 | 49 | FO1, PO4 |
| 4 | 435 | 0.77 | 0.85 | 48 | FO1, PO4 |
| 5 | 329 | 0.52 | 0.74 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 993 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 297 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 130 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3C3D · Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8PVT6 · AlphaFold monomer V2.0 prediction for 2-phospho-L-lactate transferase (Q8PVT6) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q8PVT6
- Elsewhere: RCSB PDB 3C3D · PDBe 3C3D · UniProt Q8PVT6
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