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5hhd

Crystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vascular endothelial growth factor A

OrganismNot specified

UniProt P15692

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 D-Peptide RFX037.D × 2 GLYCEROL × 3 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1kmx 1vgh 2vgh

3 assemblies

Homodimer
1mjv 1mkg 1mkg 1mkk 1vpf 1vpf 2vpf 2vpf 2vpf 2vpf 3bdy 3qtk

15 assemblies; showing the first 12

Homotetramer
1mkg

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bj1 1cz8 1flt 1flt 1kat 1qty 1qty 1qty 1tzh 1tzi 1vpp 2qr0

54 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VEGFA_HUMAN
Isoform P15692-14
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–102； UniProt 214–315 Author chain B； PDBConstruct 1–102； UniProt 214–315

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_id5hhd
Deposition date deposition_date2016-01-10
Structure title titleCrystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21
Keywords keywords;HETEROCHIRAL PROTEIN-PROTEIN COMPLEX, D-PROTEIN ANTAGONIST, GROWTH FACTOR-INHIBITOR COMPLEX, RACEMIC CRYSTALLOGRAPHY, DE NOVO PROTEIN ;; DE NOVO PROTEIN
Experimental Method methodX-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.

5hhd__assembly_1__model_1

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

Download this curve (.dat)

5hhd__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5hhd__assembly_1__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）25.49 Å
Rg (electron density)25.28 Å
Total Rg25.92 Å
Atom count2587
Residues202
Excluded volume46370 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5hhd__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5hhd__assembly_2__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 (7)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5hhdA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id5hhdB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id5hhdG00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5hhdH00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily10 —
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7. Citations (1)