MolNFT v1 · #51370 · protein

Structures of the open and closed state of trypanosomal triosephosphate isomerase: as observed in a new crystal form: implications for the reaction mechanism

2V5L: “Structures of the open and closed state of trypanosomal triosephosphate isomerase: as observed in a new…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.56). MolNFT v1 #51370 on GenesisL1: 3D structure, binding…

PDB: 2V5L
Type: protein
Length: 498 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triosephosphate isomerase
EC: 5.3.1.1
UniProt: P04789
Ligands: SO4
Pockets: 6 · best druggability 0.56

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	249	46% helix, 16% strand	P04789

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

6 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	254	0.56	0.78	32	empty
2	109	0.46	0.79	18	empty
3	93	0.44	0.79	14	empty
4	59	0.35	0.78	16	SO4
5	53	0.31	0.77	16	SO4

Interfaces

1 interface between chains.

A–B · 172 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2V5L · Structures of the Open and Closed State of Trypanosomal Triosephosphate Isomerase: as… · the same entry in another collection · chain A against A, TM-score 1.00
4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain B against A, TM-score 1.00
4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain A against A, TM-score 1.00
P04789 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase, glycosomal (P04789) · 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 P04789
Elsewhere: RCSB PDB 2V5L · PDBe 2V5L · UniProt P04789

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