SAXSdb — 1t25

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1. Protein Identity and Related Structures Protein Identity & Related Structures

L-lactate dehydrogenase

Plasmodium falciparum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–316	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 GAG 3-HYDROXYISOXAZOLE-4-CARBOXYLIC ACID × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.186

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1T25	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CEQ CHLOROQUINE BINDS IN THE COFACTOR BINDING SITE OF PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE. Deposited 1999-03-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.238
1CET CHLOROQUINE BINDS IN THE COFACTOR BINDING SITE OF PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE. Deposited 1999-03-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	CLQ N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.05 Å R-free 0.193
1LDG PLASMODIUM FALCIPARUM L-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE Deposited 1996-09-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 OXM OXAMIC ACID × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å R-free 0.235
1T24 Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid Deposited 2004-04-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 OXQ 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.167
1T26 Plasmodium falciparum lactate dehydrogenase complexed with NADH and 4-hydroxy-1,2,5-thiadiazole-3-carboxylic acid Deposited 2004-04-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 GBD 4-HYDROXY-1,2,5-THIADIAZOLE-3-CARBOXYLIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.209
1T2C Plasmodium falciparum lactate dehydrogenase complexed with NADH Deposited 2004-04-21	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.01 Å R-free 0.184
1T2D Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and oxalate Deposited 2004-04-21	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	OXL OXALATE ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.10 Å R-free 0.152
1T2E Plasmodium falciparum lactate dehydrogenase S245A, A327P mutant complexed with NADH and oxamate Deposited 2004-04-21	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Mutation：S245A, A327P	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 OXM OXAMIC ACID × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.191
1U4O Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedicarboxylic acid Deposited 2004-07-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–316（315 aa）	Not recorded	NDD 2,6-DICARBOXYNAPHTHALENE × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.181
1U4S Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedisulphonic acid Deposited 2004-07-26	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–316（315 aa）	Not recorded	BIH NAPHTHALENE-2,6-DISULFONIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.188
1U5A Plasmodium falciparum lactate dehydrogenase complexed with 3,5-dihydroxy-2-naphthoic acid Deposited 2004-07-27	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–316（315 aa）	Not recorded	BIK 3,7-DIHYDROXY-2-NAPHTHOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.173
1U5C Plasmodium falciparum lactate dehydrogenase complexed with 3,7-dihydroxynaphthalene-2-carboxylic acid and NAD+ Deposited 2004-07-27	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–316（315 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 BIK 3,7-DIHYDROXY-2-NAPHTHOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.65 Å R-free 0.239
1XIV Plasmodium falciparum lactate dehydrogenase complexed with 2-({4-chloro-[hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol Deposited 2004-09-22	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–316（315 aa）	Not recorded	RB2 2-({4-CHLORO-2-[HYDROXY(METHOXY)METHYL]CYCLOHEXYL}AMINO)ETHANE-1,1,2-TRIOL × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.179
2A94 Structure of Plasmodium falciparum lactate dehydrogenase complexed to APADH. Deposited 2005-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–316（315 aa）	Not recorded	AP0 ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.50 Å R-free 0.176
2X8L Plasmodium falciparum lactate dehydrogenase apo structure Deposited 2010-03-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–316（316 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；275 K；MPD, HEPES, IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 2	Resolution 1.60 Å R-free 0.167

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LDH1_PLAFD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–316； UniProt 1–316

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1t25
Deposition date deposition_date	2004-04-20
Structure title title	Plasmodium falciparum lactate dehydrogenase complexed with NADH and 3-hydroxyisoxazole-4-carboxylic acid
Keywords keywords	protein-ligand complex, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.62 Å
Radius of gyration Rg (electron density) rg_electron	19.51 Å
Forward intensity I(0) i0	20402300.00
Molecular weight molecular_weight	34846.0 kDa
Excluded volume excluded_volume	43937 Å³
Envelope volume envelope_volume	50935 Å³
Hydration-shell volume shell_volume	21612 Å³
Envelope diameter envelope_diameter	68.2 Å
Shell Rg shell_rg	26.37 Å
Envelope Rg envelope_rg	19.79 Å
Shape Rg shape_rg	19.53 Å
Total Rg total_rg	20.41 Å
Total atoms total_atoms	2442
Residues n_residues	304
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.5 Å
Rg (real space) rg_real	20.52 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.0400e+07
I(0) uncertainty (real space) i0_real_error	2.5150e+05
Rg (reciprocal space) rg_reciprocal	20.54 Å
I(0) (reciprocal space) i0_reciprocal	20400000.0000
Solution quality estimate total_estimate	0.8885
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.339
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4350000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	L-lactate dehydrogenase
Molecular weight formula_weight	34977.6 kDa
EC 编号 ec_number	1.1.1.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2675

MAPKAKIVLVGSGMIGGVMATLIVQKNLGDVVLFDIVKNMPHGKALDTSHTNVMAYSNCKVSGSNTYDDLAGADVVIVTAGFTKAPGKSDKEWNRDDLLPLNNKIMIEIGGHIKKNCPNAFIIVVTNPVDVMVQLLHQHSGVPKNKIIGLGGVLDTSRLKYYISQKLNVCPRDVNAHIVGAHGNKMVLLKRYITVGGIPLQEFINNKLISDAELEAIFDRTVNTALEIVNLHASPYVAPAAAIIEMAESYLKDLKKVLICSTLLEGQYGHSDIFGGTPVVLGANGVEQVIELQLNSEEKAKFDEAIAETKRMKALAHHHHHH

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	3-HYDROXYISOXAZOLE-4-CARBOXYLIC ACID
Molecular weight formula_weight	129.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1t25a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.5 — LDH N-terminal domain-like

Domain ID domain_id	d1t25a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1t25A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1t25A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

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8. Citations (1)

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Unit-cell length a length_a	81.241 Å
Unit-cell length b length_b	87.185 Å
Unit-cell length c length_c	92.094 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.750 Å
R factor r_factor	0.1535
R_work r_work	0.1518
R_free r_free	0.1858

fit	/app/data/saxs_computation/t2/1t25/1t25.fit
pddf	/app/data/pr_computation/t2/1t25/1t25.pr.out
profile	/app/data/saxs_computation/t2/1t25/1t25.dat

Plasmodium falciparum lactate dehydrogenase complexed with NADH and 3-hydroxyisoxazole-4-carboxylic acid

1. Protein Identity and Related Structures Protein Identity & Related Structures

L-lactate dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction