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Dhap bound leptospira interrogans triosephosphate isomerase (litim)

Analyse Dhap bound leptospira interrogans triosephosphate isomerase (litim) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YMZ
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
Ligands: 13P, SO4
Pockets: 3 · best druggability 0.38

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	—

Ligands and binding sites

13P · 1,3-dihydroxyacetonephosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 15 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.38	0.79	22	13P, SO4
2	52	0.32	0.77	19	empty
3	71	0.30	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 1813 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

4YMZ · DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM) · 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
Elsewhere: RCSB PDB 4YMZ · PDBe 4YMZ

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