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7klr

Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide

Method: SOLUTION NMR
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific demethylase 5A

Homo sapiens

UniProt P29375

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Histone H3.1 × 1 （P68431） ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2jxj 2kgg 5e6h 5isl 5ivb 5ivc 5ive 5ivf 5ivj 5ivv 5ivy 5iw0

39 assemblies; showing the first 12

Homodimer
5k4l 6dq4 6dq5 6dq6 6dqd 6dqe

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2kgi 3gl6 5c11 5ceh 5k4l 5v9p 5v9t 7klr

8 assemblies

View Construct and Data Evidence
UniProt name KDM5A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–59； UniProt 287–344

Histone H3.1

Homo sapiens

UniProt P68431

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Lysine-specific demethylase 5A × 1 （P29375） ZINC ION × 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
2b2t 2b2u 2b2v 2b2w 2cv5 2l75 2ri7 2uxn 3a1b 3afa 3ayw 3aze

476 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name H31_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–10； UniProt 2–11

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_id7klr
Deposition date deposition_date2020-10-31
Structure title titleSolution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide
Keywords keywordsPHD, H3, Epigenetics, KDM5A, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR
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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.

7klr__assembly_1__model_1

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

Download this curve (.dat)

7klr__assembly_1__model_1 | I(q)

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

7klr__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）13.13 Å
Rg (electron density)11.90 Å
Total Rg13.16 Å
Atom count1055
Residues69
Excluded volume9581 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7klr__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 2 7klr__assembly_1__model_2 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 3 7klr__assembly_1__model_3 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 4 7klr__assembly_1__model_4 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 5 7klr__assembly_1__model_5 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 6 7klr__assembly_1__model_6 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 7 7klr__assembly_1__model_7 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 8 7klr__assembly_1__model_8 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 9 7klr__assembly_1__model_9 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 10 7klr__assembly_1__model_10 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 11 7klr__assembly_1__model_11 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 12 7klr__assembly_1__model_12 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 13 7klr__assembly_1__model_13 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 14 7klr__assembly_1__model_14 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 15 7klr__assembly_1__model_15 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 16 7klr__assembly_1__model_16 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 17 7klr__assembly_1__model_17 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 18 7klr__assembly_1__model_18 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 19 7klr__assembly_1__model_19 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
1 20 7klr__assembly_1__model_20 dimeric （2） 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)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd7klra1
Class classg — Small proteins
Fold Fold foldg.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamilyg.50.1 — FYVE/PHD zinc finger
Family Family familyg.50.1.0 — automated matches
Domain ID domain_idd7klra2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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7. Citations (1)