8YTX

Tubulin-RB3-TTL in complex with compound SI9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Tubulin-RB3-TTL in complex with compound SI9

Wu, C.Y.Wang, Y.X.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Detyrosinated tubulin alpha-1B chain
A, C
440Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
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Go to UniProtKB:  Q2XVP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin--tyrosine ligase
B, D
431Sus scrofaMutation(s): 0 
Gene Names: TTL
EC: 6.3.2.25
UniProt
Find proteins for A0A8D0VN39 (Sus scrofa)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D0VN39
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
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UniProt GroupP63043
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin--tyrosine ligase380Gallus gallusMutation(s): 0 
Gene Names: TTL
EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus)
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Entity Groups  
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UniProt GroupA0A8V0Z8P0
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

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T [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP
Query on GDP

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J [auth B],
R [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
A1D68 (Subject of Investigation/LOI)
Query on A1D68

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N [auth B],
S [auth D]
2-chloranyl-~{N}-(4-methoxyphenyl)-~{N}-methyl-thieno[2,3-d]pyrimidin-4-amine
C14 H12 Cl N3 O S
MKRYUWBRVWYRBJ-UHFFFAOYSA-N
MES
Query on MES

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K [auth B],
L [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA
Query on CA

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H [auth A],
P [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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I [auth A],
M [auth B],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.37α = 90
b = 158.307β = 90
c = 180.655γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release