8ZN8 | pdb_00008zn8

MjF-3C-CdS QDs

PDB DOI: https://doi.org/10.2210/pdb8ZN8/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Penaeus japonicus
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2024-05-26 Released: 2025-05-28
Deposition Author(s): Duan, M.P., Zhang, T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.207 (Depositor), 0.208 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Construction of an artificial photosynthesis system by incorporation of CdS quantum dots into the intrasubunit interface of a four-helix-bundle-structure enzyme

Duan, M.P., Zhang, T.

To be published.

Macromolecule Content

Total Structure Weight: 120.21 kDa
Atom Count: 8,739
Modeled Residue Count: 1,014
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C, D, E A, B, C, D, E, F	169	Penaeus japonicus	Mutation(s): 0 EC: 1.16.3.1
UniProt
Find proteins for T2B7E1 (Penaeus japonicus) Explore T2B7E1 Go to UniProtKB: T2B7E1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	T2B7E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD (Subject of Investigation/LOI) Query on CD Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SB [auth F] SDF format, chain SA [auth D] SDF format, chain RB [auth F] SDF format, chain RA [auth D] SDF format, chain QB [auth F] SDF format, chain QA [auth D] SDF format, chain PB [auth F] SDF format, chain PA [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GB [auth E] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain FB [auth E] SDF format, chain FA [auth C] SDF format, chain EB [auth E] SDF format, chain EA [auth C] SDF format, chain DB [auth E] SDF format, chain DA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SB [auth F] MOL2 format, chain SA [auth D] MOL2 format, chain RB [auth F] MOL2 format, chain RA [auth D] MOL2 format, chain QB [auth F] MOL2 format, chain QA [auth D] MOL2 format, chain PB [auth F] MOL2 format, chain PA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain FB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain EB [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain DB [auth E] MOL2 format, chain DA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SB [auth F] mmCIF format, chain SA [auth D] mmCIF format, chain RB [auth F] mmCIF format, chain RA [auth D] mmCIF format, chain QB [auth F] mmCIF format, chain QA [auth D] mmCIF format, chain PB [auth F] mmCIF format, chain PA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain FB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain EB [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain DB [auth E] mmCIF format, chain DA [auth C]	DA [auth C] DB [auth E] EA [auth C] EB [auth E] FA [auth C] DA [auth C], DB [auth E], EA [auth C], EB [auth E], FA [auth C], FB [auth E], G [auth A], GA [auth C], GB [auth E], H [auth A], I [auth A], J [auth A], PA [auth D], PB [auth F], QA [auth D], QB [auth F], RA [auth D], RB [auth F], SA [auth D], SB [auth F], T [auth B], U [auth B], V [auth B], W [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain RB [auth F] Focus chain SA [auth D] Focus chain SB [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain DA [auth C] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain RB [auth F] Focus chain SA [auth D] Focus chain SB [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain ZB [auth F] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain OB [auth E] SDF format, chain OA [auth C] SDF format, chain CB [auth D] SDF format, chain CA [auth B] MOL2 format, chain ZB [auth F] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain OA [auth C] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] mmCIF format, chain ZB [auth F] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain OB [auth E] mmCIF format, chain OA [auth C] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B]	CA [auth B] CB [auth D] OA [auth C] OB [auth E] R [auth A] CA [auth B], CB [auth D], OA [auth C], OB [auth E], R [auth A], S [auth A], ZB [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain CB [auth D] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain R [auth A] Focus chain S [auth A] Focus chain ZB [auth F] Interactions & Density Focus chain CA [auth B] Focus chain CB [auth D] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain R [auth A] Focus chain S [auth A] Focus chain ZB [auth F]
H2S (Subject of Investigation/LOI) Query on H2S Download Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain XB [auth F] SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain WB [auth F] SDF format, chain WA [auth D] SDF format, chain VB [auth F] SDF format, chain VA [auth D] SDF format, chain UB [auth F] SDF format, chain UA [auth D] SDF format, chain TB [auth F] SDF format, chain TA [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MB [auth E] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain LB [auth E] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KB [auth E] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JB [auth E] SDF format, chain JA [auth C] SDF format, chain IB [auth E] SDF format, chain IA [auth C] SDF format, chain HB [auth E] SDF format, chain HA [auth C] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth F] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WB [auth F] MOL2 format, chain WA [auth D] MOL2 format, chain VB [auth F] MOL2 format, chain VA [auth D] MOL2 format, chain UB [auth F] MOL2 format, chain UA [auth D] MOL2 format, chain TB [auth F] MOL2 format, chain TA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth E] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth F] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WB [auth F] mmCIF format, chain WA [auth D] mmCIF format, chain VB [auth F] mmCIF format, chain VA [auth D] mmCIF format, chain UB [auth F] mmCIF format, chain UA [auth D] mmCIF format, chain TB [auth F] mmCIF format, chain TA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth E] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain HB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] HA [auth C] HB [auth E] IA [auth C] AA [auth B], BA [auth B], HA [auth C], HB [auth E], IA [auth C], IB [auth E], JA [auth C], JB [auth E], K [auth A], KA [auth C], KB [auth E], L [auth A], LA [auth C], LB [auth E], M [auth A], MA [auth C], MB [auth E], N [auth A], O [auth A], P [auth A], TA [auth D], TB [auth F], UA [auth D], UB [auth F], VA [auth D], VB [auth F], WA [auth D], WB [auth F], X [auth B], XA [auth D], XB [auth F], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain UA [auth D] Focus chain UB [auth F] Focus chain VA [auth D] Focus chain VB [auth F] Focus chain WA [auth D] Focus chain WB [auth F] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain TA [auth D] Focus chain TB [auth F] Focus chain UA [auth D] Focus chain UB [auth F] Focus chain VA [auth D] Focus chain VB [auth F] Focus chain WA [auth D] Focus chain WB [auth F] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain YB [auth F] SDF format, chain Q [auth A] SDF format, chain NB [auth E] SDF format, chain NA [auth C] SDF format, chain BB [auth D] SDF format, chain AB [auth D] MOL2 format, chain YB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain BB [auth D] MOL2 format, chain AB [auth D] mmCIF format, chain YB [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain NB [auth E] mmCIF format, chain NA [auth C] mmCIF format, chain BB [auth D] mmCIF format, chain AB [auth D]	AB [auth D] BB [auth D] NA [auth C] NB [auth E] Q [auth A] AB [auth D], BB [auth D], NA [auth C], NB [auth E], Q [auth A], YB [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain Q [auth A] Focus chain YB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain Q [auth A] Focus chain YB [auth F]