9F69: Triosephosphate isomerase

Name: PDB 9F69: Crystal structure of human triose phosphate isomerase with methyl malonic acid ligand
Published: 2025-03-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: isomerase

Crystal structure of human triose phosphate isomerase with methyl malonic acid ligand. Determined by X-ray diffraction at 1.17 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 1.17 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,168
Mol. weight: 26.51 kDa
Ligands: DXX
Released: 12 Mar 2025

Explore 9F69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F69 contains 16 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
α-helix	19-31	13
α-helix	34-35	2
β-strand	38-43	6	1
α-helix	46-48	3
α-helix	49-55	7
β-strand	61-64	4	1
α-helix	81-86	6
β-strand	91-94	4	1
α-helix	97-101	5
α-helix	107-119	13
β-strand	123-128	6	1
α-helix	132-136	5
α-helix	140-152	13
α-helix	158-160	3
β-strand	161-165	5	1
α-helix	168-170	3
α-helix	179-196	18
α-helix	199-204	6
β-strand	207-209	3	1
α-helix	218-222	5
β-strand	229-232	4	1
α-helix	234-237	4
α-helix	240-245	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Triosephosphate isomerase	A	protein	245	Homo sapiens	P60174 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9F69_1 Triosephosphate isomerase (chains A)
RKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAA
QNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGV
IACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQE
VHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDI
INAKQ

Ligands and cofactors

ID	Name	Formula	Copies
DXX	Methylmalonic acid	C4 H6 O4	1

Water and common crystallization additives (BR) are not listed.

Primary citation

Human glycolysis isomerases are inhibited by weak metabolite modulators. Jonatansdottir, Y.Y., Rolfsson, O., Hjorleifsson, J.G. FEBS J (2025) 292:3180-3204. DOI 10.1111/febs.70049 · PubMed

Other PDB entries of the same protein (UniProt P60174 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FFC 1.25 Å, Crystal structure of human triose phosphate isomerase with glycerol-3-phosphate ligand
7RDE 1.31 Å, Human Triose Phosphate Isomerase Q181P
4UNL 1.5 Å, Crystal structure of a single mutant (N71D) of triosephosphate isomerase from human
4POC 1.6 Å, Structure of Triosephosphate Isomerase Wild Type human enzyme.
6UPF 1.65 Å, Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure
4ZVJ 1.7 Å, Structure of human triose phosphate isomerase K13M
2JK2 1.7 Å, Structural basis of human triosephosphate isomerase deficiency. Crystal structure of the…
6UP1 1.83 Å, Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure
2VOM 1.85 Å, Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and…
4BR1 1.9 Å, Protease-induced heterodimer of human triosephosphate isomerase.
6UP5 1.92 Å, Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure
1KLU 1.93 Å, Crystal structure of HLA-DR1/TPI(23-37) complexed with staphylococcal enterotoxin C3…

Browse structure collections

About this viewer

MolViewer shows 9F69 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.