7Y74

Apostichopus japonicus ferritin mutant-D129A/E132A

PDB DOI: https://doi.org/10.2210/pdb7Y74/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Apostichopus japonicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-06-21 Released: 2023-07-12
Deposition Author(s): Wu, Y., Ming, T.H., Su, X.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.220
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Apostichopus japonicus ferritin mutant-D129A/E132A

Wu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 242.96 kDa
Atom Count: 17,989
Modelled Residue Count: 2,045
Deposited Residue Count: 2,076
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, G, H, I, J, K, L	173	Apostichopus japonicus	Mutation(s): 2 Gene Names: BSL78_19566 EC: 1.16.3.1
UniProt
Find proteins for Q2QJV4 (Stichopus japonicus) Explore Q2QJV4 Go to UniProtKB: Q2QJV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2QJV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DB [auth K] SDF format, chain FA [auth E] SDF format, chain HB [auth L] SDF format, chain JA [auth F] SDF format, chain NA [auth G] SDF format, chain P [auth A] SDF format, chain RA [auth H] SDF format, chain T [auth B] SDF format, chain VA [auth I] SDF format, chain X [auth C] SDF format, chain ZA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain HB [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain ZA [auth J]	BA [auth D] DB [auth K] FA [auth E] HB [auth L] JA [auth F] BA [auth D], DB [auth K], FA [auth E], HB [auth L], JA [auth F], NA [auth G], P [auth A], RA [auth H], T [auth B], VA [auth I], X [auth C], ZA [auth J]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain P [auth A] Focus chain RA [auth H] Focus chain T [auth B] Focus chain VA [auth I] Focus chain X [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain P [auth A] Focus chain RA [auth H] Focus chain T [auth B] Focus chain VA [auth I] Focus chain X [auth C] Focus chain ZA [auth J]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain CA [auth E] SDF format, chain CB [auth K] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain EB [auth L] SDF format, chain FB [auth L] SDF format, chain GA [auth F] SDF format, chain GB [auth L] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain QA [auth H] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth I] SDF format, chain TA [auth I] SDF format, chain U [auth C] SDF format, chain UA [auth I] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain WA [auth J] SDF format, chain XA [auth J] SDF format, chain Y [auth D] SDF format, chain YA [auth J] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain CB [auth K] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth L] MOL2 format, chain FB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth L] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth J] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth J] MOL2 format, chain Z [auth D]	AA [auth D] AB [auth K] BB [auth K] CA [auth E] CB [auth K] AA [auth D], AB [auth K], BB [auth K], CA [auth E], CB [auth K], DA [auth E], EA [auth E], EB [auth L], FB [auth L], GA [auth F], GB [auth L], HA [auth F], IA [auth F], KA [auth G], LA [auth G], M [auth A], MA [auth G], N [auth A], O [auth A], OA [auth H], PA [auth H], Q [auth B], QA [auth H], R [auth B], S [auth B], SA [auth I], TA [auth I], U [auth C], UA [auth I], V [auth C], W [auth C], WA [auth J], XA [auth J], Y [auth D], YA [auth J], Z [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain CB [auth K] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth C] Focus chain UA [auth I] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth J] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain YA [auth J] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain CB [auth K] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth C] Focus chain UA [auth I] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth J] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain YA [auth J] Focus chain Z [auth D]