3MPX | pdb_00003mpx

Crystal structure of the DH and PH-1 domains of human FGD5

PDB DOI: https://doi.org/10.2210/pdb3MPX/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-27 Released: 2010-06-23
Deposition Author(s): Shen, Y., Nedyalkova, L., Tong, Y., Tempel, W., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.289 (Depositor), 0.297 (DCC)
R-Value Work:
0.218 (Depositor), 0.225 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the DH and PH-1 domains of human FGD5

Shen, Y., Nedyalkova, L., Tong, Y., Tempel, W., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 50.3 kDa
Atom Count: 2,298
Modeled Residue Count: 303
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FYVE, RhoGEF and PH domain-containing protein 5	A	434	Homo sapiens	Mutation(s): 0 Gene Names: FGD5, ZFYVE23
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZNL6 (Homo sapiens) Explore Q6ZNL6 Go to UniProtKB: Q6ZNL6
PHAROS: Q6ZNL6 GTEx: ENSG00000154783
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ZNL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] 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] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] 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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.289 (Depositor), 0.297 (DCC)
R-Value Work: 0.218 (Depositor), 0.225 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.14	α = 90
b = 70.645	β = 90
c = 127.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-06-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary