MolNFT v1 · #110854 · protein

Crystal structure of triosephosphate isomerase from gemmata obscuriglobus

4Y96: “Crystal structure of triosephosphate isomerase from gemmata obscuriglobus”. X-ray diffraction, 3 ligands (NA, CA, PO4), 6 pockets (best druggability 0.40). MolNFT v1 #110854 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4Y96
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: NA, CA, PO4
Pockets: 6 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Triosephosphate isomerase (EC 5.3.1.1)	protein	250	49% helix, 16% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B
CA · Calcium ion · metal · chains A
PO4 · Phosphate 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.40	0.76	24	empty
2	74	0.38	0.78	14	empty
3	84	0.37	0.76	14	empty
4	72	0.34	0.76	15	NA
5	75	0.33	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 808 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4Y96 · Crystal structure of Triosephosphate Isomerase from Gemmata obscuriglobus · 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 4Y96 · PDBe 4Y96

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