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Structure of SHMT2 in complex with cbx

Analyse Structure of SHMT2 in complex with cbx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BYI
Type: protein
Length: 925 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serine hydroxymethyltransferase, mitochondrial
EC: 2.1.2.1
UniProt: P34897
Ligands: CBO, PO4
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1)	protein	463	45% helix, 13% strand	P34897
B	Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1)	protein	462	46% helix, 13% strand	P34897

Ligands and binding sites

CBO · Carbenoxolone · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	488	0.76	0.84	30	CBO
2	66	0.74	0.98	18	empty
3	579	0.71	0.80	55	CBO, PO4
4	228	0.52	0.76	32	empty
5	181	0.49	0.77	24	empty

Interfaces

1 interface between chains.

A–B · 4607 Å² buried · 65 hydrogen bonds · protein-protein

Compared structures

7BYI · Structure of SHMT2 in complex with CBX · the same entry in another collection · chain A against A, TM-score 1.00
P34897 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P34897
Elsewhere: RCSB PDB 7BYI · PDBe 7BYI · UniProt P34897

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