5ylj

Crystal structure of T2R-TTL-Millepachine complex

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

Tubulin alpha-1B chain

Sus scrofa

UniProt Q2XVP4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Tubulin beta chain × 2 (A0A287AGU7) Stathmin-4 × 1 (P63043) Tubulin tyrosine ligase × 1 (E1BQ43) GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)prop-2-en-1-one × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name TBA1B_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451 Author chain C; PDBConstruct 1–451; UniProt 1–451

Tubulin beta chain

Sus scrofa

UniProt A0A287AGU7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Tubulin alpha-1B chain × 2 (Q2XVP4) Stathmin-4 × 1 (P63043) Tubulin tyrosine ligase × 1 (E1BQ43) GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)prop-2-en-1-one × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name A0A287AGU7_PIG
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–445; UniProt 1–445 Author chain D; PDBConstruct 1–445; UniProt 1–445

Stathmin-4

Rattus norvegicus

UniProt P63043

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Tubulin alpha-1B chain × 2 (Q2XVP4) Tubulin beta chain × 2 (A0A287AGU7) Tubulin tyrosine ligase × 1 (E1BQ43) GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)prop-2-en-1-one × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name STMN4_RAT
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 3–143; UniProt 49–189

Tubulin tyrosine ligase

Gallus gallus

UniProt E1BQ43

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Tubulin alpha-1B chain × 2 (Q2XVP4) Tubulin beta chain × 2 (A0A287AGU7) Stathmin-4 × 1 (P63043) GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)prop-2-en-1-one × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name E1BQ43_CHICK
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 1–378; UniProt 1–378

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_id5ylj
Deposition date deposition_date2017-10-17
Structure title titleCrystal structure of T2R-TTL-Millepachine complex
Keywords keywordscolchicine binding domain, tubulin inhibitor, tublin, Millepachine, STRUCTURAL PROTEIN; STRUCTURAL 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.

5ylj__assembly_1__model_1

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

Download this curve (.dat)

5ylj__assembly_1__model_1 | I(q)

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

5ylj__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)56.14 Å
Rg (electron density)57.01 Å
Total Rg56.81 Å
Atom count17506
Residues2181
Excluded volume309680 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5ylj__assembly_1__model_1 hexameric (6) 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 (13)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd5ylja1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5ylja2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5yljb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5yljb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5yljc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5yljc2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5yljd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5yljd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5ylje_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.10 — Stathmin
Family Family familya.137.10.1 — Stathmin
Domain ID domain_idd5yljf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.30 — PreATP-grasp domain
Superfamily Superfamily superfamilyc.30.1 — PreATP-grasp domain
Family Family familyc.30.1.9 — Tubulin tyrosine ligase (TTL) N-terminal domain-like
Domain ID domain_idd5yljf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.10 — Tubulin tyrosine ligase (TTL) C-terminal domain-like
Domain ID domain_idd5yljf3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id5yljA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id5yljA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id5yljA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5yljB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id5yljB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id5yljB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5yljC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id5yljC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id5yljC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5yljD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id5yljD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id5yljD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5yljE01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id5yljF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11480 —
Domain ID domain_id5yljF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id5yljF03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
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7. Citations (1)