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7dp8

Crystal structure of T2R-TTL-Cevipabulin-eribulin complex

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

Tubulin alpha-1B chain

OrganismNot specified

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 × 5 CALCIUM ION × 6 GLYCEROL × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;6-[2,6-bis(fluoranyl)-4-[3-(methylamino)propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine ; × 2 ;(1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name) ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6 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
3j8x 3j8y 3jak 3jal 3jar 3jas 3jat 3jaw 4zhq 4zi7 4zol 5ca0

244 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TBA1B_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–450； UniProt 1–450 Author chain C； PDBConstruct 1–450； UniProt 1–450

Tubulin beta chain

OrganismNot specified

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 × 5 CALCIUM ION × 6 GLYCEROL × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;6-[2,6-bis(fluoranyl)-4-[3-(methylamino)propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine ; × 2 ;(1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name) ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6 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
5xiw 5xkf 5xkg 5yl2 5ylj 5yls 6br1 6brf 6bry 6bs2 6d88 6kpp

99 assemblies; showing the first 12

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 × 5 CALCIUM ION × 6 GLYCEROL × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;6-[2,6-bis(fluoranyl)-4-[3-(methylamino)propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine ; × 2 ;(1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name) ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6 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
1sa0 1z2b 3du7 3e22 3hkb 3hkc 3hkd 3hke 3n2g 3n2k 3ryc 3ryf

288 assemblies; showing the first 12

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 × 5 CALCIUM ION × 6 GLYCEROL × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;6-[2,6-bis(fluoranyl)-4-[3-(methylamino)propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine ; × 2 ;(1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name) ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6 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
4i4t 4i50 4i55 4ihj 4iij 4o2a 4o2b 4o4h 4o4i 4o4j 4o4l 4tuy

242 assemblies; showing the first 12

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_id7dp8
Deposition date deposition_date2020-12-18
Structure title titleCrystal structure of T2R-TTL-Cevipabulin-eribulin complex
Keywords keywordstubulin inhibitor, tublin, 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.

7dp8__assembly_1__model_1

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

Download this curve (.dat)

7dp8__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.

7dp8__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）55.77 Å
Rg (electron density)56.70 Å
Total Rg56.48 Å
Atom count34637
Residues2196
Excluded volume312590 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7dp8__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 (14)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd7dp8c1
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_idd7dp8c2
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_idd7dp8e_
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_idd7dp8f1
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_idd7dp8f2
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_idd7dp8f3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id7dp8F01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11480 —
Domain ID domain_id7dp8F02
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
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7. Citations (1)