9GVU | pdb_00009gvu

Human Rab27A in complex with cyclic peptide IMP-2660

PDB DOI: https://doi.org/10.2210/pdb9GVU/pdb

Classification: EXOCYTOSIS
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-09-25 Released: 2025-10-15
Deposition Author(s): Petracca, R., Tersa, M., De Vita, E., Morgan, M.R., Cota, E., Tate, E.W.
Funding Organization(s): Cancer Research UK, H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (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

A potent macrocyclic peptide modulator of Rab27a identified by RaPID screening

Petracca, R., Tersa, M., De Vita, E., Morgan, M.R., Cota, E., Tate, E.W.

To be published.

Macromolecule Content

Total Structure Weight: 47.73 kDa
Atom Count: 3,388
Modeled Residue Count: 395
Deposited Residue Count: 396
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-27A	A, B	184	Homo sapiens	Mutation(s): 3 Gene Names: 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51159
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic peptide IMP-2660	C [auth D], D [auth F]	14	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B]	M [auth A], T [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain M [auth A] Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain U [auth D] SDF format, chain V [auth F] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain V [auth F] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth D] mmCIF format, chain V [auth F] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth D], V [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth D] Focus chain V [auth F] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth D] Focus chain V [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	E [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.232 (Depositor), 0.235 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.357	α = 90
b = 72.714	β = 90
c = 91.658	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C29637/A20781
Cancer Research UK	United Kingdom	C29637/A26892
H2020 Marie Curie Actions of the European Commission	European Union	797995