Research workbench

Triosephosphate isomerase of vibrio marinus

Analyse Triosephosphate isomerase of vibrio marinus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AW2
Type: protein
Length: 2,036 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triosephosphate isomerase
EC: 5.3.1.1
UniProt: P50921
Ligands: SO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J	Triosephosphate isomerase (EC 5.3.1.1)	protein	255	49% helix, 15% strand	P50921
B, E, H, K	Triosephosphate isomerase (EC 5.3.1.1)	protein	254	48% helix, 15% strand	P50921

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, D, G, J

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	156	0.73	0.92	39	empty
2	166	0.72	0.90	41	empty
3	160	0.71	0.90	43	empty
4	184	0.71	0.89	45	empty
5	129	0.52	0.81	24	empty

Interfaces

11 interfaces between chains.

J–K · 1725 Å² buried · 36 hydrogen bonds · protein-protein
G–H · 1723 Å² buried · 36 hydrogen bonds · protein-protein
D–E · 1722 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 1721 Å² buried · 36 hydrogen bonds · protein-protein
D–J · 419 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1AW2 · Triosephosphate isomerase of vibrio marinus · the same entry in another collection · chain K against K, TM-score 1.00
P50921 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P50921) · a predicted model of the same protein · chain B 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 P50921
Elsewhere: RCSB PDB 1AW2 · PDBe 1AW2 · UniProt P50921

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