6EKK | pdb_00006ekk

Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state.

PDB DOI: https://doi.org/10.2210/pdb6EKK/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2017-09-26 Released: 2018-10-17
Deposition Author(s): Srikannathasan, V., Szykowska, A., Tallant, C., Strain-Damerell, C., Kopec, J., Kupinska, K., Mukhopadhyay, S., Gavin, M., Wang, D., Chalk, R., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Huber, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.232 (Depositor), 0.234 (DCC)
R-Value Work:
0.194 (Depositor), 0.198 (DCC)
R-Value Observed:
0.195 (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

Crystal structure of DENND1A-RAB35 complex with GDP bound state.

Srikannathasan, V.

To be published.

Macromolecule Content

Total Structure Weight: 132.42 kDa
Atom Count: 9,750
Modeled Residue Count: 1,106
Deposited Residue Count: 1,138
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DENN domain-containing protein 1A	A, B	393	Homo sapiens	Mutation(s): 0 Gene Names: DENND1A, FAM31A, KIAA1608
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEH3 (Homo sapiens) Explore Q8TEH3 Go to UniProtKB: Q8TEH3
PHAROS: Q8TEH3 GTEx: ENSG00000119522
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TEH3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-35	C, D	176	Homo sapiens	Mutation(s): 0 Gene Names: RAB35, RAB1C, RAY EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15286 (Homo sapiens) Explore Q15286 Go to UniProtKB: Q15286
PHAROS: Q15286 GTEx: ENSG00000111737
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15286
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	T [auth C], W [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain T [auth C] Focus chain W [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	E [auth A] F [auth A] J [auth B] K [auth B] L [auth B] E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], Q [auth C], R [auth C], U [auth D], V [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] 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 S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] 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 S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] 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 S [auth C]	G [auth A] H [auth A] I [auth A] M [auth B] N [auth B] G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]