Research workbench

Substrate mimic bound to sgtam

Analyse Substrate mimic bound to sgtam in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RJR
Type: protein
Length: 1,052 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine aminomutase
EC: 5.4.3.6
UniProt: Q8GMG0
Ligands: 295
Pockets: 10 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tyrosine aminomutase (EC 5.4.3.6)	protein	526	58% helix, 7% strand	Q8GMG0

Ligands and binding sites

295 · (2S,3S)-3-(4-fluorophenyl)-2,3-dihydroxypropanoic acid · ligand · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	158	0.62	0.84	32	empty
2	107	0.52	0.82	27	295
3	162	0.51	0.78	35	empty
4	138	0.39	0.74	27	empty
5	92	0.39	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 4903 Å² buried · 83 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

Q8GMG0 · AlphaFold monomer V2.0 prediction for mio-dependent tyrosine 2,3-aminomutase (Q8GMG0) · a predicted model of the same protein · chain A against A, TM-score 1.00
2RJR · Substrate mimic bound to SgTAM · the same entry in another collection · chain B against B, 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 Q8GMG0
Elsewhere: RCSB PDB 2RJR · PDBe 2RJR · UniProt Q8GMG0

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