6QD5 | pdb_00006qd5

X-ray Structure of the Human Urea Channel SLC14A1/UT1

PDB DOI: https://doi.org/10.2210/pdb6QD5/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTM

Deposited: 2018-12-31 Released: 2019-01-09
Deposition Author(s): Dietz, L., Chi, G., Pike, A.C.W., Moreau, C., Man, H., Snee, M., Scacioc, A., Shrestha, L., Mukhopadhyay, S.M.M., Mckinley, G., Ellis, K., Kliszcak, M., Chalk, R., Borkowska, O., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Durr, K.L., Structural Genomics Consortium (SGC)
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

X-ray Structure of the Human Urea Channel SLC14A1/UT1

Dietz, L., Chi, G., Pike, A.C.W., Moreau, C., Man, H., Snee, M., Scacioc, A., Shrestha, L., Mukhopadhyay, S.M.M., Mckinley, G., Ellis, K., Kliszcak, M., Chalk, R., Borkowska, O., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Durr, K.L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 43.1 kDa
Atom Count: 2,974
Modelled Residue Count: 356
Deposited Residue Count: 367
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea transporter 1	A	367	Homo sapiens	Mutation(s): 3 Gene Names: SLC14A1, HUT11, JK, RACH1, UT1, UTE Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q13336 (Homo sapiens) Explore Q13336 Go to UniProtKB: Q13336
PHAROS: Q13336 GTEx: ENSG00000141469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13336
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [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]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		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] 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]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.331	α = 90
b = 112.331	β = 90
c = 87.94	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-09

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
European Commission		115766

Revision History (Full details and data files)

Version 1.0: 2019-01-09
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-24
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary