MolNFT v1 · #189128 · protein
Complex structure of serine hydroxymethyltransferase from enterococcus faecium and its inhibitor
7V3D: “Complex structure of serine hydroxymethyltransferase from enterococcus faecium and its inhibitor”. X-ray diffraction, 3 ligands (5M5, PLP, CL), 9 pockets (best druggability 0.79). MolNFT v1 #189128 on GenesisL1: 3D structure…
- PDB
- 7V3D
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- A0A133CK16
- Ligands
- 5M5, PLP, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 409 | 50% helix, 14% strand | A0A133CK16 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 411 | 50% helix, 14% strand | A0A133CK16 |
Ligands and binding sites
- 5M5 · (4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.79 | 0.90 | 48 | 5M5, PLP, CL |
| 2 | 350 | 0.78 | 0.88 | 57 | 5M5, PLP, CL |
| 3 | 330 | 0.66 | 0.81 | 40 | empty |
| 4 | 249 | 0.49 | 0.74 | 36 | empty |
| 5 | 70 | 0.37 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3570 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7V3D · Complex structure of serine hydroxymethyltransferase from Enterococcus faecium and its… · 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 A0A133CK16
- Elsewhere: RCSB PDB 7V3D · PDBe 7V3D · UniProt A0A133CK16
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