7ZOF | pdb_00007zof

Streptavidin Iron-Porphyrin

PDB DOI: https://doi.org/10.2210/pdb7ZOF/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-04-25 Released: 2022-07-13
Deposition Author(s): Igareta, N.V., Ward, T.R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.203 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Streptavidin Iron-Porphyrin

Igareta, N.V.

To be published.

Macromolecule Content

Total Structure Weight: 68.1 kDa
Atom Count: 4,003
Modeled Residue Count: 490
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	158	Streptomyces avidinii	Mutation(s): 2
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JLL (Subject of Investigation/LOI) Query on JLL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	(2R)-2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3-[[(5Z,10Z,14Z,19Z)-15-[[[(2R)-2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3-sulfo-propanoyl]amino]methyl]-1,4,21,23-tetrahydroporphyrin-5-yl]methylamino]-3-oxidanylidene-propane-1-sulfonic acid C₄₈ H₆₀ N₁₂ O₁₂ S₄ GOHRVMOEJJKEAR-NBUULTOJSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	F [auth A], H [auth B], I [auth C], K [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain K [auth D]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	J [auth C], L [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain J [auth C] Focus chain L [auth D]