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 = "Shanmugaratnam, 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 45 Structures.

Refinements

Structure Determination Methodology

experimental (45)

Scientific Name of Source Organism

	Escherichia coli K-12 (17)
	Escherichia coli (12)
	synthetic construct (10)
	Thermotoga maritima (3)
	Escherichia coli 55989 (1)
	Saccharomyces cerevisiae S288C (1)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (1)
	Thermotoga maritima MSB8 (1)

Taxonomy

	Bacteria (34)
	other sequences (10)
	Eukaryota (1)

Experimental Method

	X-RAY DIFFRACTION (44)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (45)

Refinement Resolution (Å)

	1.0 - 1.5 (16)
	1.5 - 2.0 (20)
	2.0 - 2.5 (6)
	2.5 - 3.0 (2)

Release Date

	2010 - 2014 (1)
	2015 - 2019 (13)
	2020 - 2024 (31)

Enzyme Classification Name

Lyases (1)

Symmetry Type

	Asymmetric (29)
	Cyclic (17)

SCOP Classification

	All alpha proteins (13)
	Alpha and beta proteins (a/b) (9)
	Artifacts (2)

AllSelected

1 to 25 of 45 Structures

Page 1 of 2

Sort by

Explore in 3D

2LLE \| pdb_00002lle	Download File View File

Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds

Coles, M., Truffault, V., Eisenbeis, S., Proffitt, W., Meiler, J., Hocker, B.

(2012) J Am Chem Soc 134: 4019-4022

Released	2012-03-21
Method	SOLUTION NMR
Organisms	Thermotoga maritima
Macromolecule	Chemotaxis protein CheY, Imidazole glycerol phosphate synthase subunit HisF chimera (protein)

Explore in 3D

5OWF \| pdb_00005owf	Download File View File

Structure of a LAO-binding protein mutant with glutamine

Shanmugaratnam, S., Banda-Vazquez, J., Sosa-Peinado, A., Hocker, B.

(2018) Protein Sci 27: 957-968

Released	2018-03-21
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Macromolecule	Lysine/arginine/ornithine-binding periplasmic protein (protein)
Unique Ligands	EDO, GLN, GOL, PEG

Explore in 3D

6EJW \| pdb_00006ejw	Download File View File

Tryptophan Repressor TrpR from E.coli wildtype with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IAC

Explore in 3D

6EJZ \| pdb_00006ejz	Download File View File

Tryptophan Repressor TrpR from E.coli variant S88Y with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli 55989
Macromolecule	Trp operon repressor (protein)
Unique Ligands	EDO, IAC, SO4

Explore in 3D

6EKP \| pdb_00006ekp	Download File View File

Tryptophan Repressor TrpR from E.coli variant T44L T81M S88Y with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-01-30
Method	X-RAY DIFFRACTION 1.46 Å
Organisms	Escherichia coli K-12
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IAC, P3G

Explore in 3D

6ELB \| pdb_00006elb	Download File View File

Tryptophan Repressor TrpR from E.coli variant M42F T44L T81M N87G S88Y with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.437 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IAC

Explore in 3D

6ELF \| pdb_00006elf	Download File View File

Tryptophan Repressor TrpR from E.coli variant M42F T44L T81I S88Y with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.832 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IAC

Explore in 3D

6ELG \| pdb_00006elg	Download File View File

Tryptophan Repressor TrpR from E.coli variant M42F T44L T81I S88Y with Indole-3-acetonitrile

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.38 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	3BO

Explore in 3D

6ENI \| pdb_00006eni	Download File View File

Tryptophan Repressor TrpR from E.coli variant T44L S88Y with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	EDO, IAC

Explore in 3D

6ENN \| pdb_00006enn	Download File View File

Tryptophan Repressor TrpR from E.coli variant T44L T81M N87G S88Y with Indole-3-acetic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Herud-Sikimic, O., Juergens, G., Hocker, B.

(2021) Nature

Released	2019-02-06
Method	X-RAY DIFFRACTION 1.17 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IAC

Explore in 3D

6F7F \| pdb_00006f7f	Download File View File

Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid

Stiel, A.C., Shanmugaratnam, S., Hocker, B.

To be published

Released	2019-03-27
Method	X-RAY DIFFRACTION 2.128 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IOP

Explore in 3D

6F7G \| pdb_00006f7g	Download File View File

Tryptophan Repressor TrpR from E.coli with 5-Methyltryptamine

Stiel, A.C., Shanmugaratnam, S., Hocker, B.

To be published

Released	2018-12-19
Method	X-RAY DIFFRACTION 1.656 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	CVW

Explore in 3D

6F9K \| pdb_00006f9k	Download File View File

Tryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan as ligand

Stiel, A.C., Shanmugaratnam, S., Hocker, B.

To be published

Released	2019-01-30
Method	X-RAY DIFFRACTION 1.399 Å
Organisms	Escherichia coli K-12
Macromolecule	Trp operon repressor (protein)
Unique Ligands	D0Q, SO4

Explore in 3D

6FAL \| pdb_00006fal	Download File View File

Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid as ligand

Stiel, A.C., Shanmugaratnam, S., Hocker, B.

To be published

Released	2019-01-30
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Escherichia coli
Macromolecule	Trp operon repressor (protein)
Unique Ligands	IOP

Explore in 3D

6SLD \| pdb_00006sld	Download File View File

Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol

Berger, J., Fitz, M., Johnen, P., Shanmugaratnam, S., Hocker, B., Stiel, A.C., Schaaf, G.

To be published

Released	2020-08-19
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	CRAL-TRIO domain-containing protein YKL091C (protein)
Unique Ligands	B7N

Explore in 3D

6YE0 \| pdb_00006ye0	Download File View File

E.coli's Putrescine receptor PotF complexed with Putrescine

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	JFN, ONT, ONW, PUT

Explore in 3D

6YE6 \| pdb_00006ye6	Download File View File

E.coli's Putrescine receptor PotF complexed with Agmatine

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	AG2, CL, JFN, ONT, ONW, SO4

Explore in 3D

6YE7 \| pdb_00006ye7	Download File View File

E.coli's Putrescine receptor PotF complexed with Cadaverine

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	1PE, CL, EDO, MLI, N2P, P33, PEG, PG4, PGE, TAM

Explore in 3D

6YE8 \| pdb_00006ye8	Download File View File

E.coli's Putrescine receptor PotF complexed with Spermidine

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	CL, JFN, ONT, SO4, SPD

Explore in 3D

6YEB \| pdb_00006yeb	Download File View File

E.coli's Putrescine receptor PotF in its closed apo state

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	CL, EDO, GOL, PEG, PGE, SO4

Explore in 3D

6YEC \| pdb_00006yec	Download File View File

E.coli's Putrescine receptor PotF complexed with Spermine

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	CL, EDO, GOL, PEG, PG4, PGE, SO4, SPM

Explore in 3D

6YED \| pdb_00006yed	Download File View File

E.coli's Putrescine receptor PotF in its open apo state

Shanmugaratnam, S., Kroeger, P., Hocker, B.

(2021) Structure 29: 433

Released	2021-01-20
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Escherichia coli K-12
Macromolecule	Putrescine-binding periplasmic protein (protein)
Unique Ligands	CL, EDO, PEG, PGE

Explore in 3D

6YQX \| pdb_00006yqx	Download File View File

Crystal structure of DeNovoTIM13, a de novo designed TIM barrel

Romero-Romero, S., Kordes, S., Shanmugaratnam, S., Fernandez-Velasco, D.A., Hocker, B.

(2021) J Mol Biology 433: 167153-167153

Released	2021-07-21
Method	X-RAY DIFFRACTION 1.638 Å
Organisms	synthetic construct
Macromolecule	de novo designed TIM barrel DeNovoTIM13 (protein)
Unique Ligands	CL, GOL