RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Citation Author = "Deep, S."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 12 Structures.

Refinements

Structure Determination Methodology

experimental (12)

Scientific Name of Source Organism

	Klebsiella pneumoniae (5)
	Escherichia coli (2)
	Severe acute respiratory syndrome coronavirus 2 (2)
	Staphylococcus aureus (1)
	Staphylococcus aureus subsp. aureus NCTC 8325 (1)
	synthetic construct (1)

Taxonomy

	Bacteria (9)
	Riboviria (2)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (10)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

Protein (12)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (1)
	2.0 - 2.5 (2)
	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2015 - 2019 (2)
	2020 - 2024 (6)
	2025 - 2029 (4)

Enzyme Classification Name

	Hydrolases (5)
	Oxidoreductases (2)

Symmetry Type

	Asymmetric (10)
	Cyclic (2)

AllSelected

1 to 12 of 12 Structures

Page 1 of 1

Sort by

Explore in 3D

5NA1 \| pdb_00005na1	Download File View File

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

Brito, J.A., Athayde, D., Sousa, F.M., Sena, F.V., Pereira, M.M., Archer, M.

(2017) Biochim Biophys Acta 1858: 823-832

Released	2018-01-10
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325
Macromolecule	NADH dehydrogenase-like protein SAOUHSC_00878 (protein)
Unique Ligands	FAD, MLI, PO4

Explore in 3D

5NA4 \| pdb_00005na4	Download File View File

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - E172S mutant

Brito, J.A., Athayde, D., Sousa, F.M., Sena, F.V., Pereira, M.M., Archer, M.

(2017) Biochim Biophys Acta 1858: 823-832

Released	2018-01-10
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Staphylococcus aureus
Macromolecule	NADH dehydrogenase-like protein SAOUHSC_00878 (protein)
Unique Ligands	FAD

Explore in 3D

6SUT \| pdb_00006sut	Download File View File

Crystal structure of phosphothreonine MCR-2

Hinchliffe, P., Spencer, J.

(2020) Chem Commun (Camb) 56: 6874-6877

Released	2020-06-03
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Escherichia coli
Macromolecule	Putative integral membrane protein (protein)
Unique Ligands	BR, GOL, ZN

Explore in 3D

7AH0 \| pdb_00007ah0	Download File View File

Crystal structure of the de novo designed two-heme binding protein, 4D2

Hutchins, G.H., Parnell, A.E., Anderson, J.L.R.

(2023) Proc Natl Acad Sci U S A 120: e2306046120-e2306046120

Released	2021-10-06
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	synthetic construct
Macromolecule	4D2 (protein)
Unique Ligands	HEM

Explore in 3D

7OD3 \| pdb_00007od3	Download File View File

SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry

Toelzer, C., Gupta, K., Yadav, S.K.N., Borucu, U., Schaffitzel, C., Berger, I.

(2022) Nat Commun 13: 222-222

Released	2022-01-26
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	EIC, NAG

Explore in 3D

7ODL \| pdb_00007odl	Download File View File

SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry

Toelzer, C., Gupta, K., Yadav, S.K.N., Borucu, U., Schaffitzel, C., Berger, I.

(2022) Nat Commun 13: 222-222

Released	2022-01-26
Method	ELECTRON MICROSCOPY 3.03 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	EIC, NAG

Explore in 3D

8CCR \| pdb_00008ccr	Download File View File

Crystal structure of the T19D mutant of the de novo diheme binding 4D2

Barringer, R., Anderson, R.

(2023) Proc Natl Acad Sci U S A 120: e2306046120-e2306046120

Released	2023-08-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	4D2 (mutant T19D) (protein)
Unique Ligands	CL, HEM, LMR

Explore in 3D

8RWO \| pdb_00008rwo	Download File View File

KPC-2 G89D Mutant Apo Structure

Beer, M., Hinchliffe, P., Tooke, C.L., Spencer, J.

(2024) Chem Sci 15: 17232-17244

Released	2025-01-22
Method	X-RAY DIFFRACTION 1.13 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Carbapenem-hydrolyzing beta-lactamase KPC (protein)
Unique Ligands	GOL, SO4

Explore in 3D

8RWP \| pdb_00008rwp	Download File View File

KPC-2 G89D Mutant in Complex with Avibactam

Beer, M., Hinchliffe, P., Tooke, C.L., Spencer, J.

(2024) Chem Sci 15: 17232-17244

Released	2025-01-22
Method	X-RAY DIFFRACTION 1.19 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Carbapenem-hydrolyzing beta-lactamase KPC (protein)
Unique Ligands	A1H3M, GOL, NXL, SO4

Explore in 3D

8RWQ \| pdb_00008rwq	Download File View File

KPC-2 G89D/E166Q Mutant Apo Structure

Beer, M., Hinchliffe, P., Tooke, C.L., Spencer, J.

(2024) Chem Sci 15: 17232-17244

Released	2024-12-25
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Carbapenem-hydrolyzing beta-lactamase KPC (protein)
Unique Ligands	GOL, SO4

Explore in 3D

8RWR \| pdb_00008rwr	Download File View File

KPC-2 G89D/E166Q Mutant in Complex with Imipenem

Beer, M., Hinchliffe, P., Tooke, C.L., Spencer, J.

(2024) Chem Sci 15: 17232-17244

Released	2025-01-22
Method	X-RAY DIFFRACTION 1.03 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Carbapenem-hydrolyzing beta-lactamase KPC (protein)
Unique Ligands	A1H3N, A1H3O, GOL, SO4

Explore in 3D

8RWS \| pdb_00008rws	Download File View File

KPC-2 G89D/E166Q Mutant in Complex with Meropenem

Beer, M., Hinchliffe, P., Tooke, C.L., Spencer, J.

(2024) Chem Sci 15: 17232-17244

Released	2025-01-22
Method	X-RAY DIFFRACTION 1.09 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Carbapenem-hydrolyzing beta-lactamase KPC (protein)
Unique Ligands	MER, O2F, SO4

1 to 12 of 12 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

5NA1 | pdb_00005na1

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

5NA4 | pdb_00005na4

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - E172S mutant

6SUT | pdb_00006sut

Crystal structure of phosphothreonine MCR-2

7AH0 | pdb_00007ah0

Crystal structure of the de novo designed two-heme binding protein, 4D2

7OD3 | pdb_00007od3

SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry

7ODL | pdb_00007odl

SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry

8CCR | pdb_00008ccr

Crystal structure of the T19D mutant of the de novo diheme binding 4D2

8RWO | pdb_00008rwo

KPC-2 G89D Mutant Apo Structure

8RWP | pdb_00008rwp

KPC-2 G89D Mutant in Complex with Avibactam

8RWQ | pdb_00008rwq

KPC-2 G89D/E166Q Mutant Apo Structure

8RWR | pdb_00008rwr

KPC-2 G89D/E166Q Mutant in Complex with Imipenem

8RWS | pdb_00008rws

KPC-2 G89D/E166Q Mutant in Complex with Meropenem

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

5NA1 | pdb_00005na1

5NA4 | pdb_00005na4

6SUT | pdb_00006sut

7AH0 | pdb_00007ah0

7OD3 | pdb_00007od3

7ODL | pdb_00007odl

8CCR | pdb_00008ccr

8RWO | pdb_00008rwo

8RWP | pdb_00008rwp

8RWQ | pdb_00008rwq

8RWR | pdb_00008rwr

8RWS | pdb_00008rws