9KZL | pdb_00009kzl

Crystal structure of the functional unit (HtH1-h) of hemocyanin from Haliotis discus hannai,Containing a met site

PDB DOI: https://doi.org/10.2210/pdb9KZL/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Haliotis discus hannai
Mutation(s): No

Deposited: 2024-12-10 Released: 2025-01-15
Deposition Author(s): Zhao, G.H., Yang, H.C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (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

Crystal structure of the functional unit (HtH1-h) of hemocyanin from Haliotis discus hannai,Containing a met state

Zhao, G.H., Yang, H.C.

To be published.

Macromolecule Content

Total Structure Weight: 171.06 kDa
Atom Count: 13,080
Modeled Residue Count: 1,467
Deposited Residue Count: 1,467
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemocyanin type 1	A	489	Haliotis discus hannai	Mutation(s): 0
UniProt
Find proteins for A0A7R6RYX0 (Haliotis discus hannai) Explore A0A7R6RYX0 Go to UniProtKB: A0A7R6RYX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R6RYX0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemocyanin type 1	B, C	489	Haliotis discus hannai	Mutation(s): 0
UniProt
Find proteins for A0A7R6RYX0 (Haliotis discus hannai) Explore A0A7R6RYX0 Go to UniProtKB: A0A7R6RYX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R6RYX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN (Subject of Investigation/LOI) Query on MAN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C]	D [auth A], I [auth B], O [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain O [auth C]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	F [auth A] G [auth A] K [auth B] L [auth B] Q [auth C] F [auth A], G [auth A], K [auth B], L [auth B], Q [auth C], R [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C]
EOH (Subject of Investigation/LOI) Query on EOH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C]	E [auth A], J [auth B], P [auth C]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C]
OH (Subject of Investigation/LOI) Query on OH Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth C] MOL2 format, chain H [auth A] MOL2 format, chain S [auth C] mmCIF format, chain H [auth A] mmCIF format, chain S [auth C]	H [auth A], S [auth C]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain S [auth C]
O (Subject of Investigation/LOI) Query on O Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	M [auth B], N [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]