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Crystal structure of rabbit muscle triosephosphate isomerase

Analyse Crystal structure of rabbit muscle triosephosphate isomerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R2R
Type: protein
Length: 987 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triosephosphate isomerase
EC: 5.3.1.1
UniProt: P00939
Ligands: MG
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Triosephosphate isomerase (EC 5.3.1.1)	protein	246	45% helix, 16% strand	P00939
B, C, D	Triosephosphate isomerase (EC 5.3.1.1)	protein	247	45% helix, 17% strand	P00939

Ligands and binding sites

MG · Magnesium ion · metal · 9 copies · chains B, C, D
DMS · Dimethyl sulfoxide · additive · 17 copies · chains A, D, B, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, D

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

Pockets

7 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	1050	0.84	0.85	118	MG, DMS
2	51	0.68	0.98	16	empty
3	131	0.51	0.80	25	MG
4	125	0.45	0.77	29	empty
5	78	0.39	0.78	19	empty

Interfaces

5 interfaces between chains.

C–D · 1775 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 1774 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 514 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 82 Å² buried · 1 hydrogen bond · protein-protein
A–D · 71 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1R2R · Crystal structure of rabbit muscle triosephosphate isomerase · the same entry in another collection · chain A against A, TM-score 1.00
P00939 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P00939) · a predicted model of the same protein · chain B 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 P00939
Elsewhere: RCSB PDB 1R2R · PDBe 1R2R · UniProt P00939

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