9KH8 | pdb_00009kh8

Co-Carbonic Anhydrase II complexed with 3NPA before UV at 100 K

PDB DOI: https://doi.org/10.2210/pdb9KH8/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-09 Released: 2025-10-22
Deposition Author(s): Kim, C.U., Kim, J.K.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.164 (Depositor), 0.168 (DCC)
R-Value Work:
0.134 (Depositor), 0.140 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Temperature series of human Carbonic Anhydrase II with photolysis of caged CO2

Kim, C.U., Kim, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 29.41 kDa
Atom Count: 2,442
Modeled Residue Count: 257
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0 Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918 Go to UniProtKB: P00918
PHAROS: P00918 GTEx: ENSG00000104267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CO (Subject of Investigation/LOI) Query on CO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.164 (Depositor), 0.168 (DCC)
R-Value Work: 0.134 (Depositor), 0.140 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.191	α = 90
b = 41.22	β = 104.25
c = 72.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Korea, Republic Of	SSTF-BA1702-04 (Samsung Science and Technology Foundation)

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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.