← Back to search
6q94

Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man

Method: X-RAY DIFFRACTION
▼

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

GDP-mannose 4,6 dehydratase

Homo sapiens

UniProt O60547

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE × 4 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 4 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE × 4 1,2-ETHANEDIOL × 2 water × 2 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 4 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE × 4 1,2-ETHANEDIOL × 4 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer
1t2a 5in4 5in5 6gpj 6gpk 6gpl 6q94 6q94 6q94

9 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name GMDS_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–352； UniProt 23–372 Author chain B； PDBConstruct 3–352； UniProt 23–372 Author chain C； PDBConstruct 3–352； UniProt 23–372 Author chain D； PDBConstruct 3–352； UniProt 23–372 Author chain E； PDBConstruct 3–352； UniProt 23–372 Author chain F； PDBConstruct 3–352； UniProt 23–372 Author chain G； PDBConstruct 3–352； UniProt 23–372 Author chain H； PDBConstruct 3–352； UniProt 23–372

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6q94
Deposition date deposition_date2018-12-17
Structure title titleCrystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man
Keywords keywordsGDP-mannose 4, 6 dehydratase, fucosylation, Structural Genomics, Structural Genomics Consortium, SGC, Lyase; LYASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

6q94__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6q94__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6q94__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）33.92 Å
Rg (electron density)33.25 Å
Total Rg33.86 Å
Atom count11501
Residues1391
Excluded volume201630 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6q94__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6q94__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6q94__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6q94a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94d_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94e_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94f_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94g_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6q94h_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (16 domains)

Domain ID domain_id6q94A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94A02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94B02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94C02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94D02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94E01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94E02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94F01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94F02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94G01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94G02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
Domain ID domain_id6q94H01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6q94H02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily10 — UDP-galactose 4-epimerase, domain 1
▶

7. Citations (1)