9O0J | pdb_00009o0j

HtaA CR1 domain from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb9O0J/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-02 Released: 2025-09-03
Deposition Author(s): Ford, J., Sawaya, M.R., Clubb, R.T.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.248 (Depositor), 0.257 (DCC)
R-Value Work:
0.216 (Depositor), 0.219 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: in silico
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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

Structural Basis of Heme Scavenging by the ChtA and HtaA Hemophores in Corynebacterium diphtheriae

Ford, J., Goring, A.K., Lee, Y., Chen, M., Mahoney, B.J., Sawaya, M.R., Shafaat, H.S., Loo, J.A., Clubb, R.T.

(2025) J Biological Chem : 110633

DOI: https://doi.org/10.1016/j.jbc.2025.110633

Macromolecule Content

Total Structure Weight: 194.02 kDa
Atom Count: 14,103
Modeled Residue Count: 1,780
Deposited Residue Count: 1,780
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein HtaACR1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	178	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0 Gene Names: DIP0625
UniProt
Find proteins for Q6NIZ1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NIZ1 Go to UniProtKB: Q6NIZ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NIZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] mmCIF format, chain BA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I]	BA [auth J] K [auth A] N [auth B] O [auth C] P [auth D] BA [auth J], K [auth A], N [auth B], O [auth C], P [auth D], R [auth E], S [auth F], V [auth G], X [auth H], Y [auth I]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Y [auth I] Interactions & Density Focus chain BA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Y [auth I]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth F] MOL2 format, chain L [auth A] MOL2 format, chain T [auth F] mmCIF format, chain L [auth A] mmCIF format, chain T [auth F]	L [auth A], T [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain T [auth F] Interactions & Density Focus chain L [auth A] Focus chain T [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain W [auth G] SDF format, chain Z [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain W [auth G] mmCIF format, chain Z [auth I]	CA [auth J], W [auth G], Z [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Focus chain W [auth G] Focus chain Z [auth I] Interactions & Density Focus chain CA [auth J] Focus chain W [auth G] Focus chain Z [auth I]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain M [auth A] SDF format, chain Q [auth D] SDF format, chain U [auth F] MOL2 format, chain AA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth F] mmCIF format, chain AA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain U [auth F]	AA [auth I], M [auth A], Q [auth D], U [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain M [auth A] Focus chain Q [auth D] Focus chain U [auth F] Interactions & Density Focus chain AA [auth I] Focus chain M [auth A] Focus chain Q [auth D] Focus chain U [auth F]