MolNFT v1 · #51953 · protein

Crystal structure of N341ABSSHMT internal aldimine

2VMN · Serine hydroxymethyltransferase: “Crystal structure of N341ABSSHMT internal aldimine”. X-ray diffraction, 2 ligands (PLP, PO4), 2 pockets (best druggability 0.48). MolNFT v1 #51953 on GenesisL1: 3D structure, binding sites and…

PDB: 2VMN
Type: protein
Length: 405 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine hydroxymethyltransferase
EC: 2.1.2.1
UniProt: Q7SIB6
Ligands: PLP, PO4
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine hydroxymethyltransferase (EC 2.1.2.1)	protein	405	49% helix, 14% strand	Q7SIB6

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains A
PO4 · Phosphate ion · ion · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.48	0.76	27	empty
2	125	0.42	0.76	19	empty

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

2VMN · Crystal structure of N341AbsSHMT internal aldimine · 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 Q7SIB6
Elsewhere: RCSB PDB 2VMN · PDBe 2VMN · UniProt Q7SIB6

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