7STC | pdb_00007stc

AQP5 T41H with Ni2+

PDB DOI: https://doi.org/10.2210/pdb7STC/pdb

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

Deposited: 2021-11-12 Released: 2022-11-16
Deposition Author(s): Kowatz, T.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.310 (Depositor), 0.300 (DCC)
R-Value Work:
0.286 (Depositor), 0.270 (DCC)
R-Value Observed:
0.287 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

AQP5 T41H with Ni2+

Kowatz, T., Lodowski, D., Vahedi-Faridi, A.

To be published.

Macromolecule Content

Total Structure Weight: 113.8 kDa
Atom Count: 7,412
Modeled Residue Count: 976
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin-5	A, B, C, D	266	Homo sapiens	Mutation(s): 1 Gene Names: AQP5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P55064 (Homo sapiens) Explore P55064 Go to UniProtKB: P55064
PHAROS: P55064 GTEx: ENSG00000161798
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55064
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 2.25 Å
R-Value Free: 0.310 (Depositor), 0.300 (DCC)
R-Value Work: 0.286 (Depositor), 0.270 (DCC)
R-Value Observed: 0.287 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.681	α = 90
b = 90.649	β = 90
c = 184.767	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	N000141612535

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2022-11-30
Changes: Database references
Version 1.2: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.