2W2J | pdb_00002w2j

Crystal structure of the human carbonic anhydrase related protein VIII

PDB DOI: https://doi.org/10.2210/pdb2W2J/pdb

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

Deposited: 2008-10-31 Released: 2009-02-03
Deposition Author(s): Kramm, A., Muniz, J.R.C., Picaud, S.S., von Delft, F., Pilka, E.S., Yue, W.W., King, O.N.F., Kochan, G., Pike, A.C.W., Filippakopoulos, P., Arrowsmith, C., Wikstrom, M., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.229 (Depositor), 0.184 (DCC)
R-Value Work:
0.199 (Depositor), 0.186 (DCC)
R-Value Observed:
0.201 (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

Crystal Structure of Human Carbonic Anhydrase-Related Protein Viii Reveals the Basis for Catalytic Silencing.

Picaud, S.S., Muniz, J.R.C., Kramm, A., Pilka, E.S., Kochan, G., Oppermann, U., Yue, W.W.

(2009) Proteins 76: 507

PubMed: 19360879 Search on PubMed
DOI: https://doi.org/10.1002/prot.22411
Primary Citation Related Structures:
2W2J

Organizational Affiliation

Structural Genomics Consortium, Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 33.75 kDa
Atom Count: 2,626
Modeled Residue Count: 268
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE-RELATED PROTEIN	A	291	Homo sapiens	Mutation(s): 0 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35219 (Homo sapiens) Explore P35219 Go to UniProtKB: P35219
PHAROS: P35219 GTEx: ENSG00000178538
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35219
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [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] MOL2 format, chain J [auth A] MOL2 format, chain I [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] mmCIF format, chain J [auth A] mmCIF format, chain I [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]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions 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] Interactions & Density 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]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.229 (Depositor), 0.184 (DCC)
R-Value Work: 0.199 (Depositor), 0.186 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.267	α = 90
b = 73.854	β = 90
c = 87.908	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-03
Type: Initial release
Version 1.1: 2012-02-22
Changes: Non-polymer description, Refinement description, Structure summary, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description