SAXSdb — 6yne

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

Glyceraldehyde-3-phosphate dehydrogenase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL × 13 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3P_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–335； UniProt 1–335 Author chain B； PDBConstruct 1–335； UniProt 1–335 Author chain C； PDBConstruct 1–335； UniProt 1–335 Author chain D； PDBConstruct 1–335； UniProt 1–335

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	6yne
Deposition date deposition_date	2020-04-13
Structure title title	GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.
Keywords keywords	HEK293F, kifunensine, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6yne__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6yne__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yne__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.72 Å
Rg (electron density)	31.87 Å
Total Rg	32.64 Å
Atom count	20595
Residues	1336
Excluded volume	183650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yne__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Glyceraldehyde-3-phosphate dehydrogenase
Molecular weight formula_weight	36099.2 kDa
EC 编号 ec_number	1.2.1.12,2.6.99.-
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	21295

MGKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Entity 2 Entity 2 non-polymer

Description description	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
Molecular weight formula_weight	458.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	569

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6yneA01
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	6yneA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	6yneB01
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	6yneB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	6yneC01
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	6yneC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	6yneD01
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	6yneD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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Unit-cell length a length_a	81.787 Å
Unit-cell length b length_b	124.652 Å
Unit-cell length c length_c	79.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.853 Å
Low-resolution limit resolution_low	72.850 Å
R factor r_factor	0.1911
R_work r_work	0.1903
R_free r_free	0.2066

GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.

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

Glyceraldehyde-3-phosphate dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6yne__assembly_1__model_1

6yne__assembly_1__model_1 | I(q)

6yne__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.

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

Glyceraldehyde-3-phosphate dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6yne__assembly_1__model_1

6yne__assembly_1__model_1 | I(q)

6yne__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)