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Crystal structure of TT0473, putative triosephosphate isomerase from thermus thermophilus HB8

Analyse Crystal structure of TT0473, putative triosephosphate isomerase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YYA
Type: protein
Length: 500 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triosephosphate isomerase
EC: 5.3.1.1
UniProt: Q5SJR1
Ligands: NA, PO4
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Triosephosphate isomerase (EC 5.3.1.1)	protein	250	46% helix, 16% strand	Q5SJR1

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 7 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	143	0.61	0.85	33	empty
2	114	0.40	0.75	21	empty
3	59	0.37	0.79	25	PO4

Interfaces

1 interface between chains.

A–B · 1696 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

1YYA · Crystal structure of TT0473, putative Triosephosphate Isomerase from Thermus thermophilus… · the same entry in another collection · chain A against A, TM-score 1.00
Q5SJR1 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (Q5SJR1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q5SJR1
Elsewhere: RCSB PDB 1YYA · PDBe 1YYA · UniProt Q5SJR1

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