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6z4z

Crystal structure of CLK1 in complex with macrocycle ODS2004070

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

Dual specificity protein kinase CLK1

Homo sapiens

UniProt P49759

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 PHOSPHATE ION × 3 GLYCEROL × 1 7,10-Dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12,6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 7,10-Dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12,6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 PHOSPHATE ION × 1 7,10-Dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.12,6.017,20]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxylic acid × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1z57 2vag 5j1v 5j1v 5j1v 5j1w 5j1w 5j1w 5x8i 5x8i 6ft8 6ft9

59 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name CLK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–339； UniProt 148–484 Author chain B； PDBConstruct 3–339； UniProt 148–484 Author chain C； PDBConstruct 3–339； UniProt 148–484

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_id6z4z
Deposition date deposition_date2020-05-26
Structure title titleCrystal structure of CLK1 in complex with macrocycle ODS2004070
Keywords keywordskinase, kinase inhibitor, clk1, macrocycle, nanocyclic, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE; TRANSFERASE
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.

6z4z__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6z4z__assembly_3__model_1 | I(q)

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

6z4z__assembly_3__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）22.25 Å
Rg (electron density)21.02 Å
Total Rg21.86 Å
Atom count2787
Residues337
Excluded volume49531 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6z4z__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6z4z__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6z4z__assembly_3__model_1 monomeric （1） 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) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6z4za1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6z4za2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6z4zb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6z4zb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6z4zc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd6z4zc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id6z4zA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6z4zB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6z4zC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
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7. Citations (1)