2ABM

Crystal Structure of Aquaporin Z Tetramer Reveals both Open and Closed Water-conducting Channels

PDB DOI: https://doi.org/10.2210/pdb2ABM/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2005-07-15 Released: 2005-09-20
Deposition Author(s): Jiang, J., Daniels, B.V., Fu, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.242
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 198.42 kDa
Atom Count: 13,946
Modelled Residue Count: 1,816
Deposited Residue Count: 1,848
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 Z	A, B, C, D, E A, B, C, D, E, F, G, H	231	Escherichia coli	Mutation(s): 0 Gene Names: aqpZ, bniP Membrane Entity: Yes
UniProt
Find proteins for P60844 (Escherichia coli (strain K12)) Explore P60844 Go to UniProtKB: P60844
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60844
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Z [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G]	K [auth A] O [auth B] P [auth B] U [auth E] W [auth F] K [auth A], O [auth B], P [auth B], U [auth E], W [auth F], X [auth F], Z [auth G]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth G]
POQ Query on POQ Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	BIS(((3S,4S,5R,6R)-5-(ETHYL(PHOSPHORYLOXY))-3,4,6-TRIHYDROXY-TETRAHYDRO-2H-PYRAN-2-YL)METHYL) HYDROGEN PHOSPHATE C₁₆ H₃₃ O₂₀ P₃ QTCHWELPTUAUQX-ASCZGESISA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
AGA Query on AGA Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain S [auth C] MOL2 format, chain BA [auth G] MOL2 format, chain S [auth C]	BA [auth G], S [auth C]	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE C₁₉ H₃₆ O₁₀ P UQSXQYRZHMGKIE-DLBZAZTESA-M		Interactions Focus chain BA [auth G] Focus chain S [auth C] Interactions & Density Focus chain BA [auth G] Focus chain S [auth C]
BGL Query on BGL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain T [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain T [auth E]	I [auth A], L [auth B], M [auth B], T [auth E]	2-O-octyl-beta-D-glucopyranose C₁₄ H₂₈ O₆ BVHPDIWLWHHJPD-RKQHYHRCSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth E] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth E]
3PG Query on 3PG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain R [auth C] MOL2 format, chain AA [auth G] MOL2 format, chain R [auth C]	AA [auth G], R [auth C]	3-PHOSPHOGLYCERIC ACID C₃ H₇ O₇ P OSJPPGNTCRNQQC-UWTATZPHSA-N		Interactions Focus chain AA [auth G] Focus chain R [auth C] Interactions & Density Focus chain AA [auth G] Focus chain R [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth F] SDF format, chain Y [auth G] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth G]	N [auth B], Q [auth C], V [auth F], Y [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth F] Focus chain Y [auth G] Interactions & Density Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth F] Focus chain Y [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.242
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.152	α = 90
b = 119.152	β = 90
c = 380.394	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-09-20

Deposition Author(s):

Jiang, J.

Daniels, B.V.

Fu, D.

Revision History (Full details and data files)

Version 1.0: 2005-09-20
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2014-10-29
Changes: Non-polymer description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 2.0: 2023-08-23
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

2ABM

Crystal Structure of Aquaporin Z Tetramer Reveals both Open and Closed Water-conducting Channels

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)