6EG5 | pdb_00006eg5

The structure of SB-1-202-tubulin complex

PDB DOI: https://doi.org/10.2210/pdb6EG5/pdb

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

Deposited: 2018-08-18 Released: 2019-08-21
Deposition Author(s): Banerjee, A.K., Wang, Y., Chen, H., Miller, D., Li, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.236 (Depositor), 0.238 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The structure of SB-1-202/SB-2-204-tubulin complex

Chen, H., Wang, Y., Li, W.

To be published.

Macromolecule Content

Total Structure Weight: 265.42 kDa
Atom Count: 18,509
Modeled Residue Count: 2,210
Deposited Residue Count: 2,317
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	450	Sus scrofa	Mutation(s): 0 Gene Names: TUBA1B EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0 Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 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

Small Molecules

Ligands 9 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 S [auth C] SDF format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain G [auth A] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	G [auth A], S [auth C], V [auth D]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain S [auth C] Focus chain V [auth D]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] MOL2 format, chain BA [auth F] mmCIF format, chain BA [auth F]	BA [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain BA [auth F] Interactions & Density Focus chain BA [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
J7S Query on J7S Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain X [auth D] MOL2 format, chain R [auth B] MOL2 format, chain X [auth D] mmCIF format, chain R [auth B] mmCIF format, chain X [auth D]	R [auth B], X [auth D]	4-(2-chloropyrido[2,3-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one C₁₆ H₁₂ Cl N₅ O₂ ONXVMYQYSMSLML-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain X [auth D] Interactions & Density Focus chain R [auth B] Focus chain X [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	P [auth B], Q [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth E] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth E] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth E]	I [auth A], O [auth B], U [auth C], Y [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth F]	AA [auth F] H [auth A] N [auth B] T [auth C] W [auth D] AA [auth F], H [auth A], N [auth B], T [auth C], W [auth D], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.236 (Depositor), 0.238 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.541	α = 90
b = 158.033	β = 90
c = 181.87	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description