7K8H | pdb_00007k8h

Beta-lactamase mixed with Ceftriaxone, 50ms

PDB DOI: https://doi.org/10.2210/pdb7K8H/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-27 Released: 2021-09-22
Deposition Author(s): Pandey, S., Schmidt, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.275 (Depositor), 0.273 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.225 (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

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Pandey, S., Calvey, G., Katz, A.M., Malla, T.N., Koua, F.H.M., Martin-Garcia, J.M., Poudyal, I., Yang, J.H., Vakili, M., Yefanov, O., Zielinski, K.A., Bajt, S., Awel, S., Doerner, K., Frank, M., Gelisio, L., Jernigan, R., Kirkwood, H., Kloos, M., Koliyadu, J., Mariani, V., Miller, M.D., Mills, G., Nelson, G., Olmos, J.L.J., Sadri, A., Sato, T., Tolstikova, A., Xu, W., Ourmazd, A., Spence, J.C.H., Schwander, P., Barty, A., Chapman, H.N., Fromme, P., Mancuso, A.P., Phillips, G.N.J., Bean, R., Pollack, L., Schmidt, M.

(2021) IUCrJ 8: 878-895

DOI: https://doi.org/10.1107/S2052252521008125

Macromolecule Content

Total Structure Weight: 116.2 kDa
Atom Count: 8,363
Modeled Residue Count: 1,060
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	267	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: blaC, ERS027646_02769 EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD3 Go to UniProtKB: P9WKD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9F2 (Subject of Investigation/LOI) Query on 9F2 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	F [auth A], G [auth B], J [auth C], K [auth D]	Ceftriaxone C₁₈ H₁₈ N₈ O₇ S₃ VAAUVRVFOQPIGI-TYHRLYECSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], I [auth C], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D]