MolNFT v1 · #5710 · protein

X-ray crystal structure at 2.7 ångströms resolution of ternary complex between the Y65F mutant of E-COLI serine hydroxymethyltransferase, glycine and 5-formyl tetrahydrofolate

1EQB: “X-ray crystal structure at 2.7 ångströms resolution of ternary complex between the Y65F mutant of E-COLI…”. X-ray diffraction, 3 ligands (GLY, PLP, FFO), 19 pockets (best druggability 0.84). MolNFT v1 #5710 on GenesisL1: 3D…

PDB: 1EQB
Type: protein
Length: 1,667 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine hydroxymethyltransferase
EC: 2.1.2.1
UniProt: P00477
Ligands: GLY, PLP, FFO
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine hydroxymethyltransferase (EC 2.1.2.1)	protein	416	48% helix, 13% strand	P00477
B, C, D	Serine hydroxymethyltransferase (EC 2.1.2.1)	protein	417	48% helix, 13% strand	P00477

Ligands and binding sites

GLY · Glycine · ligand · 4 copies · chains A, B, C, D
PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 4 copies · chains A, B, D, C

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

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	575	0.84	0.90	86	GLY, PLP, FFO
2	539	0.83	0.89	84	GLY, PLP, FFO
3	245	0.78	0.91	45	GLY, PLP, FFO
4	297	0.77	0.89	57	GLY, PLP, FFO
5	224	0.71	0.87	47	empty

Interfaces

5 interfaces between chains.

C–D · 4665 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 4650 Å² buried · 52 hydrogen bonds · protein-protein
A–D · 362 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 362 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 96 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1EQB · X-ray crystal structure at 2.7 ångströms resolution of ternary complex between the Y65F… · 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 P00477
Elsewhere: RCSB PDB 1EQB · PDBe 1EQB · UniProt P00477

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