2VOM: Triosephosphate isomerase

Name: PDB 2VOM: Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation.
Published: 2008-06-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: isomerase

Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation. Determined by X-ray diffraction at 1.85 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 7,983
Mol. weight: 106.8 kDa
Released: 17 Jun 2008

Explore 2VOM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VOM contains 62 α-helices and 40 β-strands across 4 chains. 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	14	1	2
α-helix	18-30	13
α-helix	32-34	3
β-strand	37-42	6	1
α-helix	45-47	3
α-helix	48-54	7
β-strand	60-63	4	1
β-strand	72	1	3
α-helix	80-85	6
β-strand	90-93	4	1
α-helix	96-100	5
α-helix	106-118	13
β-strand	122-127	6	1
α-helix	131-135	5
α-helix	139-152	14
α-helix	157-159	3
β-strand	160-164	5	1
α-helix	167-169	3
α-helix	178-195	18
α-helix	198-203	6
β-strand	205-208	4	1
α-helix	217-221	5
β-strand	228-231	4	1
α-helix	233-236	4
α-helix	239-244	6

Chain B: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-11	6	4
β-strand	14	1	3
α-helix	18-30	13
β-strand	37-42	6	4
α-helix	45-47	3
α-helix	48-54	7
β-strand	60-63	4	4
β-strand	72	1	2
α-helix	80-85	6
β-strand	90-93	4	4
α-helix	96-100	5
α-helix	106-118	13
β-strand	122-127	6	4
α-helix	131-135	5
α-helix	139-151	13
α-helix	157-159	3
β-strand	160-164	5	4
α-helix	178-195	18
α-helix	198-203	6
β-strand	206-208	3	4
α-helix	217-222	6
β-strand	228-231	4	4
α-helix	233-236	4
α-helix	239-244	6

Chain C: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-11	6	5
β-strand	14	1	6
α-helix	18-30	13
α-helix	32-33	2
β-strand	37-42	6	5
α-helix	45-47	3
α-helix	48-54	7
β-strand	60-63	4	5
β-strand	72	1	7
α-helix	80-85	6
β-strand	90-93	4	5
α-helix	96-100	5
α-helix	106-118	13
β-strand	122-127	6	5
α-helix	131-135	5
α-helix	139-151	13
α-helix	157-159	3
β-strand	160-164	5	5
α-helix	178-195	18
α-helix	198-203	6
β-strand	206-208	3	5
α-helix	217-221	5
β-strand	228-231	4	5
α-helix	233-236	4
α-helix	239-244	6

Chain D: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	8
β-strand	14	1	7
α-helix	18-30	13
α-helix	32-34	3
β-strand	37-42	6	8
α-helix	45-47	3
α-helix	48-54	7
β-strand	60-63	4	8
β-strand	72	1	6
α-helix	80-85	6
β-strand	90-93	4	8
α-helix	96-100	5
α-helix	106-118	13
β-strand	122-127	6	8
α-helix	131-135	5
α-helix	139-151	13
α-helix	157-159	3
β-strand	160-164	5	8
α-helix	178-195	18
α-helix	198-203	6
β-strand	206-208	3	8
α-helix	217-221	5
β-strand	228-231	4	8
α-helix	233-236	4
α-helix	239-243	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Triosephosphate isomerase	A, B, C, D	protein	250	HOMO SAPIENS	P60174 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2VOM_1 TRIOSEPHOSPHATE ISOMERASE (chains A, B, C, D)
GSAPSRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPK
IAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGDSDELIGQKVAHALA
EGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATP
QQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKP
EFVDIINAKQ

Primary citation

Structural Basis of Human Triosephosphate Isomerase Deficiency: Mutation E104D is Related to Alterations of a Conserved Water Network at the Dimer Interface. Rodriguez-Almazan, C., Arreola-Alemon, R., Rodriguez-Larrea, D. et al. J Biol Chem (2008) 283:23254. DOI 10.1074/JBC.M802145200 · PubMed

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

9F69 1.17 Å, Crystal structure of human triose phosphate isomerase with methyl malonic acid ligand
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
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

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