5XI5 | pdb_00005xi5

Crystal structure of T2R-TTL-PO5 complex

PDB DOI: https://doi.org/10.2210/pdb5XI5/pdb

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

Deposited: 2017-04-26 Released: 2017-10-18
Deposition Author(s): Chu, Y., Wang, Y., Yang, J., Li, W.
Funding Organization(s): Qingdao science and technology bureau

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.265 (Depositor), 0.260 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Synthesis, biological evaluation and X-ray structure of anti-microtubule agents

Chu, Y., Wang, Y., Yang, J., Li, W.

To be published.

Macromolecule Content

Total Structure Weight: 269.9 kDa
Atom Count: 17,473
Modeled Residue Count: 2,151
Deposited Residue Count: 2,358
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0R4I993
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0R4I995
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	184	Rattus norvegicus	Mutation(s): 0 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin tyrosine ligase	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	G [auth A], P [auth C], S [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth C] Focus chain S [auth D]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F] mmCIF format, chain V [auth F]	V [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PN6 Query on PN6 Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain U [auth D] MOL2 format, chain O [auth B] MOL2 format, chain U [auth D] mmCIF format, chain O [auth B] mmCIF format, chain U [auth D]	O [auth B], U [auth D]	(3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione C₁₉ H₂₀ N₄ O₂ UNRCMCRRFYFGFX-TYPNBTCFSA-N		Interactions Focus chain O [auth B] Focus chain U [auth D] Interactions & Density Focus chain O [auth B] Focus chain U [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B]	L [auth B], N [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain L [auth B] Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C]	I [auth A], M [auth B], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	H [auth A], K [auth B], Q [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D]