8P3K | pdb_00008p3k

Fusion hSlp2-a_Rab27A non-covalent complex with compound IMP-2505

PDB DOI: https://doi.org/10.2210/pdb8P3K/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2023-05-17 Released: 2024-11-20
Deposition Author(s): De Vita, E., Brustur, D., Tersa, M., Petracca, R., Morgan, R.M.L., Lanyon-Hogg, T., Norman, J.C., Cota, E., Tate, E.W.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.315 (Depositor), 0.315 (DCC)
R-Value Work:
0.238 (Depositor), 0.241 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Targeted covalent inhibitors of the small GTPase Rab27A

De Vita, E., Brustur, D., Tersa, M., Petracca, R., Morgan, R.M.L., Lanyon-Hogg, T., Norman, J.C., Cota, E., Tate, E.W.

To be published.

Macromolecule Content

Total Structure Weight: 54.64 kDa
Atom Count: 3,565
Modeled Residue Count: 421
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-like protein 2,Ras-related protein Rab-27A	A, B	230	Homo sapiens	Mutation(s): 3 Gene Names: SYTL2, KIAA1597, SGA72M, SLP2, SLP2A, RAB27A, RAB27 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51159 (Homo sapiens) Explore P51159 Go to UniProtKB: P51159
PHAROS: P51159 GTEx: ENSG00000069974
Find proteins for Q9HCH5 (Homo sapiens) Explore Q9HCH5 Go to UniProtKB: Q9HCH5
PHAROS: Q9HCH5 GTEx: ENSG00000137501
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P51159 Q9HCH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
WTB (Subject of Investigation/LOI) Query on WTB Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	(2~{S})-~{N}-(3-methoxyphenyl)-1-[4-(prop-2-enoylamino)phenyl]sulfonyl-pyrrolidine-2-carboxamide C₂₁ H₂₃ N₃ O₅ S NFMLSESUYLVCKE-IBGZPJMESA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth B] E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain I [auth A]	I [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain R [auth B]