5YL4

CRYSTAL STRUCTURE OF T2R-TTL-8WR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Design, synthesis and biological activity evaluation of plinabulin derivatives based on co-crystal structure

Fu, Z.Y.Li, W.B.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chainA, C450Sus barbatusMutation(s): 0 
UniProt
Find proteins for A0A0R4I993 (Sus barbatus)
Explore A0A0R4I993 
Go to UniProtKB:  A0A0R4I993
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4I993
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB, D445Sus barbatusMutation(s): 0 
UniProt
Find proteins for A0A0R4I995 (Sus barbatus)
Explore A0A0R4I995 
Go to UniProtKB:  A0A0R4I995
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4I995
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups  
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UniProt GroupP63043
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin tyrosine ligaseF384Gallus gallusMutation(s): 0 
Gene Names: TTL
UniProt
Find proteins for E1BQ43 (Gallus gallus)
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Go to UniProtKB:  E1BQ43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1BQ43
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

Download Ideal Coordinates CCD File 
U [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
J [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
8WR
Query on 8WR

Download Ideal Coordinates CCD File 
O [auth B](3Z,6Z)-3-[(4-tert-butyl-1H-imidazol-5-yl)methylidene]-6-[[3-(phenylcarbonyl)phenyl]methylidene]piperazine-2,5-dione
C26 H24 N4 O3
UOGLYILRMWEYRW-NMGXZBPKSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
L [auth B],
N [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
R [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
Q [auth C],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.461α = 90
b = 157.73β = 90
c = 182.147γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
16-5-1-61-jchChina--

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release