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3ztd

pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate

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

TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2

HOMO SAPIENS

UniProt Q15370

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 2c9w 2izv 2jz3 2ma9 3dcg

479 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ELOB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–118； UniProt 1–118 Author chain D； PDBConstruct 1–118； UniProt 1–118 Author chain G； PDBConstruct 1–118； UniProt 1–118 Author chain J； PDBConstruct 1–118； UniProt 1–118

TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1

HOMO SAPIENS

UniProt Q15369

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR × 1 （P40337） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 2c9w 2izv 2ma9 3dcg 3dcg

468 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ELOC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–97； UniProt 17–112 Author chain E； PDBConstruct 2–97； UniProt 17–112 Author chain H； PDBConstruct 2–97； UniProt 17–112 Author chain K； PDBConstruct 2–97； UniProt 17–112

VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR

HOMO SAPIENS

UniProt P40337

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 × 1 （Q15370） TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 × 1 （Q15369） METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1lm8 1lqb 1lqb 1vcb 1vcb 1vcb 1vcb 3zrc 3zrc 3zrc 3zrc 3zrf

364 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VHL_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–162； UniProt 54–213 Author chain F； PDBConstruct 3–162； UniProt 54–213 Author chain I； PDBConstruct 3–162； UniProt 54–213 Author chain L； PDBConstruct 3–162； UniProt 54–213

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_id3ztd
Deposition date deposition_date2011-07-07
Structure title titlepVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate
Keywords keywordsTRANSCRIPTION, TUMOUR SUPRESSOR PROTEIN, PVHL E3 UBIQUITIN LIGASE; TRANSCRIPTION
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.

3ztd__assembly_1__model_1

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

Download this curve (.dat)

3ztd__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.

3ztd__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）24.60 Å
Rg (electron density)23.69 Å
Total Rg24.32 Å
Atom count2567
Residues327
Excluded volume45810 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ztd__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3ztd__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3ztd__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3ztd__assembly_4__model_1 trimeric （3） 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 (5)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd3ztda_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3ztdb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.1 — BTB/POZ domain
Domain ID domain_idd3ztdc_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.3 — VHL
Family Family familyb.3.3.1 — VHL
Domain ID domain_idd3ztdd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3ztde_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.1 — BTB/POZ domain
Domain ID domain_idd3ztdf_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.3 — VHL
Family Family familyb.3.3.1 — VHL
Domain ID domain_idd3ztdg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3ztdh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.1 — BTB/POZ domain
Domain ID domain_idd3ztdi_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.3 — VHL
Family Family familyb.3.3.1 — VHL
Domain ID domain_idd3ztdj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd3ztdk_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.1 — BTB/POZ domain
Domain ID domain_idd3ztdl_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.3 — VHL
Family Family familyb.3.3.1 — VHL

CATH v4.4 (16 domains)

Domain ID domain_id3ztdA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3ztdB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3ztdC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily780 — von Hippel-Lindau disease tumour suppressor, beta domain
Domain ID domain_id3ztdC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily10 — von Hippel-Lindau disease tumour suppressor, alpha domain
Domain ID domain_id3ztdD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3ztdE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3ztdF01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily780 — von Hippel-Lindau disease tumour suppressor, beta domain
Domain ID domain_id3ztdF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily10 — von Hippel-Lindau disease tumour suppressor, alpha domain
Domain ID domain_id3ztdG00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3ztdH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3ztdI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily780 — von Hippel-Lindau disease tumour suppressor, beta domain
Domain ID domain_id3ztdI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily10 — von Hippel-Lindau disease tumour suppressor, alpha domain
Domain ID domain_id3ztdJ00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3ztdK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3ztdL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily780 — von Hippel-Lindau disease tumour suppressor, beta domain
Domain ID domain_id3ztdL02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology750 — Elongin C; Chain C, domain 1
Homologous superfamily homologous superfamily10 — von Hippel-Lindau disease tumour suppressor, alpha domain
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7. Citations (1)