SAXSdb — 9itd

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

C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–301 Chain B； UniProt 2–301	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 A1L22 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2, Morpheus Precipitant Mix 4	Resolution 2.28 Å R-free 0.299
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–301 Chain D； UniProt 2–301	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 A1L22 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2, Morpheus Precipitant Mix 4	Resolution 2.28 Å R-free 0.299

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 9ITD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A4I HUMAN TETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE Deposited 1998-01-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–300（300 aa） Chain B 1–300（300 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.50 Å R-free 0.235
1DIA HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY249543 Deposited 1999-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–306（306 aa） Chain B 1–306（306 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 L24 [[[2-AMINO-5,6,7,8-TETRAHYDRO-4-HYDROXY-PYRIDO[2,3-D]PYRIMIDIN-6-YL]-ETHYL]-PHENYL]-CARBONYL-GLUTAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 2.20 Å R-free 0.264
1DIB HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY345899 Deposited 1999-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–306（306 aa） Chain B 1–306（306 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 L34 4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 2.70 Å R-free 0.240
1DIG HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY374571 Deposited 1999-11-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–306（306 aa） Chain B 1–306（306 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 L37 [[N'-(2,5-DIAMINO-6-HYDROXY-PYRIMIDIN-4-YL)-UREAYL]-PHEN-4-YL]-CARBONYL-GLUTAMIC ACID × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 2.20 Å R-free 0.267
6ECP The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP and inhibitor LY249543 Deposited 2018-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–296（296 aa） Chain B 1–296（296 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 21V N-(4-{2-[(6S)-2-amino-4-oxo-1,4,5,6,7,8-hexahydropyrido[2,3-d]pyrimidin-6-yl]ethyl}benzoyl)-L-glutamic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K	Resolution 2.20 Å R-free 0.227
6ECQ The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP and inhibitor LY345899 Deposited 2018-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–296（296 aa） Chain B 1–296（296 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 LUD N-{4-[(6aR)-3-amino-1,9-dioxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]benzene-1-carbonyl}-L-glutamic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K.	Resolution 2.70 Å R-free 0.247
6ECR The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP Deposited 2018-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–296（296 aa） Chain B 1–296（296 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K.	Resolution 2.20 Å R-free 0.219
9ISE Human MTHFD1 in complex with LY374571 Deposited 2024-07-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–301（300 aa） Chain B 2–301（300 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 9L9 (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2 pH 7.5, Morpheus Precipitant Mix 4	Resolution 1.99 Å R-free 0.241
9ISE Human MTHFD1 in complex with LY374571 Deposited 2024-07-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–301（300 aa） Chain D 2–301（300 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 9L9 (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2 pH 7.5, Morpheus Precipitant Mix 4	Resolution 1.99 Å R-free 0.241
9ISL Human MTHFD1 in complex with compound 16e Deposited 2024-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–301（301 aa） Chain B 1–301（301 aa） Chain C 1–301（301 aa） Chain D 1–301（301 aa）	Not recorded	A1L23 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]-3-chloranyl-phenyl]carbonylamino]pentanedioic acid × 4 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.09 M NPS, Morpheus Buffer System 2 pH 7.5, 42% Morpheus Precipitant Mix 4	Resolution 2.06 Å R-free 0.250
9ISR Human MTHFD1 in complex with compound 16g Deposited 2024-07-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–301（300 aa） Chain B 2–301（300 aa）	Not recorded	A1L24 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]-3-chloranyl-phenyl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2, Morpheus Precipitant Mix 4	Resolution 2.50 Å R-free 0.264
9ISR Human MTHFD1 in complex with compound 16g Deposited 2024-07-18	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–301（300 aa） Chain D 2–301（300 aa）	Not recorded	A1L24 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]-3-chloranyl-phenyl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2, Morpheus Precipitant Mix 4	Resolution 2.50 Å R-free 0.264
9IUO Human MTHFD1 in complex with compound 16d Deposited 2024-07-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–301（300 aa） Chain B 2–301（300 aa）	Not recorded	A1L25 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]-3-methyl-phenyl]carbonylamino]pentanedioic acid × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2, Morpheus Precipitant Mix 4	Resolution 2.09 Å R-free 0.259
9IUO Human MTHFD1 in complex with compound 16d Deposited 2024-07-22	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–301（300 aa） Chain D 2–301（300 aa）	Not recorded	A1L25 (2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]-3-methyl-phenyl]carbonylamino]pentanedioic acid × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；NPS, Morpheus Buffer System 2, Morpheus Precipitant Mix 4	Resolution 2.09 Å R-free 0.259

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C1TC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–300； UniProt 2–301 Author chain B； PDBConstruct 1–300； UniProt 2–301 Author chain C； PDBConstruct 1–300； UniProt 2–301 Author chain D； PDBConstruct 1–300； UniProt 2–301

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	9itd
Deposition date deposition_date	2024-07-19
最后修订 last_revision	2025-01-01
Structure title title	Human MTHFD1 in complex with compound 16a
Keywords keywords	MTHFD1, methylenetetrahydrofolate dehydrogenase/cyclohydrolase, 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	34.37 Å
Radius of gyration Rg (electron density) rg_electron	34.10 Å
Forward intensity I(0) i0	514496000.00
Molecular weight molecular_weight	119380.0 kDa
Excluded volume excluded_volume	113710 Å³
Envelope volume envelope_volume	203450 Å³
Hydration-shell volume shell_volume	49612 Å³
Envelope diameter envelope_diameter	117.5 Å
Shell Rg shell_rg	40.95 Å
Envelope Rg envelope_rg	33.77 Å
Shape Rg shape_rg	34.13 Å
Total Rg total_rg	34.39 Å
Total atoms total_atoms	9000
Residues n_residues	1152
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	112.5 Å
Rg (real space) rg_real	34.34 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	5.1450e+08
I(0) uncertainty (real space) i0_real_error	7.5900e+06
Rg (reciprocal space) rg_reciprocal	34.36 Å
I(0) (reciprocal space) i0_reciprocal	514500000.0000
Solution quality estimate total_estimate	0.8879
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.6 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	78530000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.873

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed
Molecular weight formula_weight	33590.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9180

APAEILNGKEISAQIRARLKNQVTQLKEQVPGFTPRLAILQVGNRDDSNLYINVKLKAAEEIGIKATHIKLPRTTTESEVMKYITSLNEDSTVHGFLVQLPLDSENSINTEEVINAIAPEKDVDGLTSINAGRLARGDLNDCFIPCTPKGCLELIKETGVPIAGRHAVVVGRSKIVGAPMHDLLLWNNATVTTCHSKTAHLDEEVNKGDILVVATGQPEMVKGEWIKPGAIVIDCGINYVPDDKKPNGRKVVGDVAYDEAKERASFITPVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGLEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;(2~{S})-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]-4-(1~{H}-1,2,3,4-tetrazol-5-yl)butanoic acid ;
Molecular weight formula_weight	457.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

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8. Citations (1)

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Unit-cell length a length_a	65.296 Å
Unit-cell length b length_b	200.343 Å
Unit-cell length c length_c	239.744 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	26.210 Å
R factor r_factor	0.2399
R_work r_work	0.2368
R_free r_free	0.2993

fit	/app/data/saxs_computation/it/9itd/9itd.fit
pddf	/app/data/pr_computation/it/9itd/9itd.pr.out
profile	/app/data/saxs_computation/it/9itd/9itd.dat

Human MTHFD1 in complex with compound 16a

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

C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed

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