MolNFT v1 · #190430 · protein
Crystal structure of E. faecium shmt in complex with me-thf and plp- gly
7X5O · Serine hydroxymethyltransferase: “Crystal structure of E. faecium shmt in complex with me-thf and plp- gly”. X-ray diffraction, 2 ligands (THH, PLG), 11 pockets (best druggability 0.77). MolNFT v1 #190430 on GenesisL1: 3D structure…
- PDB
- 7X5O
- Type
- protein
- Length
- 823 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
- THH, PLG
- Pockets
- 11 · best druggability 0.77
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 | 411 | 49% helix, 14% strand | A0A133CK16 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 412 | 50% helix, 14% strand | A0A133CK16 |
Ligands and binding sites
- THH · N-[4-({[(6S)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 3 copies · chains A, B
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.77 | 0.90 | 48 | THH, PLG |
| 2 | 292 | 0.76 | 0.89 | 52 | THH, PLG |
| 3 | 317 | 0.66 | 0.81 | 38 | empty |
| 4 | 115 | 0.38 | 0.74 | 19 | empty |
| 5 | 69 | 0.36 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3650 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 7X5O · Crystal structure of E. faecium SHMT in complex with Me-THF and PLP-Gly · 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 7X5O · PDBe 7X5O · UniProt A0A133CK16
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