2EUK

Crystal Structure of Human Glycolipid Transfer Protein complexed with 24:1 Galactosylceramide

PDB DOI: https://doi.org/10.2210/pdb2EUK/pdb

Classification: LIPID TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-10-28 Released: 2006-11-14
Deposition Author(s): Malinina, L., Malakhova, M.L., Kanack, A.T., Abagyan, R., Brown, R.E., Patel, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.230
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 24.84 kDa
Atom Count: 1,892
Modelled Residue Count: 204
Deposited Residue Count: 209
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycolipid transfer protein	A	209	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZD2 (Homo sapiens) Explore Q9NZD2 Go to UniProtKB: Q9NZD2
PHAROS: Q9NZD2 GTEx: ENSG00000139433
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NZD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NER Query on NER Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(15E)-TETRACOS-15-ENOIC ACID C₂₄ H₄₆ O₂ GWHCXVQVJPWHRF-KTKRTIGZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SPH Query on SPH Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SPHINGOSINE C₁₈ H₃₇ N O₂ WWUZIQQURGPMPG-MSOLQXFVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.230
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.867	α = 90
b = 49.304	β = 122.61
c = 68.655	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

2EUK

Crystal Structure of Human Glycolipid Transfer Protein complexed with 24:1 Galactosylceramide

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)