5YL4 | pdb_00005yl4

CRYSTAL STRUCTURE OF T2R-TTL-8WR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb5YL4/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Sus barbatus, Rattus norvegicus, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-17 Released: 2017-11-15 
• Deposition Author(s): Fu, Z.Y., Li, W.B., Chu, Y.Y., Hou, Y.W., Ji, C.P.
• Funding Organization(s): 16-5-1-61-jch

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.256 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

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

Fu, Z.Y., Li, W.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 264.87 kDa 
• Atom Count: 17,466 
• Modeled Residue Count: 2,151 
• Deposited Residue Count: 2,317 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A, C	450	Sus barbatus	Mutation(s): 0
UniProt
Find proteins for A0A0R4I993 (Sus barbatus) Explore A0A0R4I993  Go to UniProtKB:  A0A0R4I993

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Sus barbatus	Mutation(s): 0
UniProt
Find proteins for A0A0R4I995 (Sus barbatus) Explore A0A0R4I995  Go to UniProtKB:  A0A0R4I995

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0  Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043  Go to UniProtKB:  P63043

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	384	Gallus gallus	Mutation(s): 0  Gene Names: TTL

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	G [auth A], P [auth C], S [auth D]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	J [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
8WR	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
MES	L [auth B], N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	I [auth A], M [auth B], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth A], K [auth B], Q [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.256 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.461	α = 90
b = 157.73	β = 90
c = 182.147	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Fu, Z.Y., Li, W.B., Chu, Y.Y., Hou, Y.W., Ji, C.P.

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Funding Organization	Location	Grant Number
16-5-1-61-jch	China	--

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations, Refinement description