8D1X | pdb_00008d1x

Crystal Structure of aminopeptidase A from Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb8D1X/pdb

Classification: HYDROLASE
Organism(s): Neisseria gonorrhoeae NCCP11945
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-27 Released: 2022-06-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.203 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of aminopeptidase A from Neisseria gonorrhoeae

Abendroth, J., DeBouver, N.D., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 308.34 kDa
Atom Count: 21,162
Modeled Residue Count: 2,809
Deposited Residue Count: 2,856
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cytosol aminopeptidase	A, B, C, D, E A, B, C, D, E, F	476	Neisseria gonorrhoeae NCCP11945	Mutation(s): 0 Gene Names: pepA, NGK_0283 EC: 3.4.11.1 (PDB Primary Data), 3.4.11.10 (PDB Primary Data)
UniProt
Find proteins for B4RJ22 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RJ22 Go to UniProtKB: B4RJ22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4RJ22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth F]	AA [auth F] I [auth A] M [auth B] Q [auth C] T [auth D] AA [auth F], I [auth A], M [auth B], Q [auth C], T [auth D], W [auth E]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain AA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth F]	BA [auth F], J [auth A], N [auth B], X [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain X [auth E]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A] K [auth B] O [auth C] R [auth D] U [auth E] G [auth A], K [auth B], O [auth C], R [auth D], U [auth E], Y [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain Y [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A] L [auth B] P [auth C] S [auth D] V [auth E] H [auth A], L [auth B], P [auth C], S [auth D], V [auth E], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F]