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: Structure Keywords HAS EXACT PHRASE "DE NOVO PROTEIN"

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 1,696 Structures.

Refinements

Structure Determination Methodology

experimental (1,696)

Scientific Name of Source Organism

	synthetic construct (1,226)
	Homo sapiens (127)
	Escherichia coli (37)
	unidentified (23)
	Heloderma suspectum (18)
	Gallus gallus (13)
	Borreliella burgdorferi (10)
	Streptococcus mutans (8)
	Aquifex aeolicus VF5 (7)
	Staphylococcus aureus (7)

More...

Taxonomy

	other sequences (1,230)
	Eukaryota (210)
	Bacteria (137)
	unclassified sequences (23)
	Archaea (15)
	Riboviria (13)
	Eukaryota (eukaryotes) (7)
	Monodnaviria (4)
	Duplodnaviria (1)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (1,260)
	SOLUTION NMR (365)
	ELECTRON MICROSCOPY (66)
	SOLID-STATE NMR (4)
	NEUTRON DIFFRACTION (1)
	POWDER DIFFRACTION (1)

Polymer Entity Type

	Protein (1,696)
	DNA (4)
	RNA (1)

Refinement Resolution (Å)

	0.5 - 1.0 (39)
	1.0 - 1.5 (238)
	1.5 - 2.0 (391)
	2.0 - 2.5 (345)
	2.5 - 3.0 (168)
	3.0 - 3.5 (82)
	3.5 - 4.0 (33)
	4.0 - 4.5 (18)
	> 4.5 (13)

Release Date

	1995 - 1999 (5)
	2000 - 2004 (74)
	2005 - 2009 (94)
	2010 - 2014 (278)
	2015 - 2019 (468)
	2020 - 2024 (748)
	2025 - 2029 (29)

Enzyme Classification Name

	Hydrolases (36)
	Transferases (21)
	Lyases (10)
	Ligases (2)
	Oxidoreductases (2)

Membrane Protein Annotation

	mpstruc (2)
	OPM (3)

Symmetry Type

	Asymmetric (1,065)
	Cyclic (498)
	Dihedral (97)
	Tetrahedral (34)
	Helical (11)
	Icosahedral (9)
	Octahedral (9)

SCOP Classification

	Designed proteins (78)
	Alpha and beta proteins (a+b) (30)
	All beta proteins (24)
	Artifacts (24)
	Coiled coil proteins (7)
	Alpha and beta proteins (a/b) (12)
	All alpha proteins (4)
	Peptides (4)
	Small proteins (2)

AllSelected

1 to 25 of 1,696 Structures

Page 1 of 68

Sort by

Explore in 3D

1BYZ \| pdb_00001byz	Download File View File

DESIGNED PEPTIDE ALPHA-1, P1 FORM

Prive, G.G., Anderson, D.H., Wesson, L., Cascio, D., Eisenberg, D.

(1999) Protein Sci 8: 1400-1409

Released	1998-10-28
Method	X-RAY DIFFRACTION 0.9 Å
Organisms	synthetic construct
Macromolecule	PROTEIN (SYNTHETIC DESIGNED PEPTIDE "ALPHA-1") (protein)
Unique Ligands	CL, ETA, MPD, MRD

Explore in 3D

1C3T \| pdb_00001c3t	Download File View File

ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY

Lazar, G.A., Johnson, E.C., Desjarlais, J.R., Handel, T.M.

(1999) Protein Sci 8: 2598-2610

Released	1999-08-20
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN (1D8 UBIQUITIN) (protein)

Explore in 3D

1CQ0 \| pdb_00001cq0	Download File View File

SOLUTION STRUCTURE OF A HUMAN HYPOCRETIN-2/OREXIN-B'SOLUTION STRUCTURE OF A HUMAN HYPOCRETIN-2/OREXIN-B '

Lee, K.-H., Bang, E.J., Chae, K.-J., Lee, D.W., Lee, W.

(1999) Eur J Biochem 266: 831-839

Released	2000-01-10
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	PROTEIN (NEW HYPOTHALAMIC NEUROPEPTIDE/OREXIN-B28) (protein)

Explore in 3D

1D7T \| pdb_00001d7t	Download File View File

NMR STRUCTURE OF AN ENGINEERED CONTRYPHAN CYCLIC PEPTIDE (MOTIF CPXXPXC)

Pallaghy, P.K., Norton, R.S.

(2000) Biopolymers 54: 173-179

Released	2000-09-13
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	YNK-CONTRYPHAN (protein)

Explore in 3D

1DJF \| pdb_00001djf	Download File View File

NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE

Montserret, R., McLeish, M.J., Bockmann, A., Geourjon, C., Penin, F.

(2000) Biochemistry 39: 8362-8373

Released	1999-12-10
Method	SOLUTION NMR
Macromolecule	GLN-ALA-PRO-ALA-TYR-LYS-LYS-ALA-ALA-LYS-LYS-LEU-ALA-GLU-SER (protein)

Explore in 3D

1DN3 \| pdb_00001dn3	Download File View File

NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL BASIC PEPTIDE

Montserret, R., McLeish, M.J., Bockmann, A., Geourjon, C., Penin, F.

(2000) Biochemistry 39: 8362-8373

Released	2000-01-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HUMAN PLATELET FACTOR 4, SEGMENT 59-73 (protein)

Explore in 3D

1DNG \| pdb_00001dng	Download File View File

NMR STRUCTURE OF A MODEL HYDROPHILIC AMPHIPATHIC HELICAL ACIDIC PEPTIDE

montserret, R., McLeish, M.J., Bockmann, A., Geourjon, C., Penin, F.

(2000) Biochemistry 39: 8362-8373

Released	2000-01-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	HUMAN PLATELET FACTOR 4, SEGMENT 59-73 (protein)

Explore in 3D

1E0M \| pdb_00001e0m	Download File View File

PROTOTYPE WW domain

Macias, M.J., Gervais, V., Civera, C., Oschkinat, H.

(2000) Nat Struct Biol 7: 375

Released	2000-04-20
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	WWPROTOTYPE (protein)

Explore in 3D

1EC5 \| pdb_00001ec5	Download File View File

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL

Geremia, S.

(2000) Proc Natl Acad Sci U S A 97: 6298-6305

Released	2000-07-26
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	PROTEIN (FOUR-HELIX BUNDLE MODEL) (protein)
Unique Ligands	ZN

Explore in 3D

1FME \| pdb_00001fme	Download File View File

SOLUTION STRUCTURE OF FSD-EY, A NOVEL PEPTIDE ASSUMING A BETA-BETA-ALPHA FOLD

Sarisky, C.A., Mayo, S.L.

(2001) J Mol Biology 307: 1411-1418

Released	2001-04-21
Method	SOLUTION NMR
Macromolecule	FSD-EY PEPTIDE (protein)

Explore in 3D

1G6U \| pdb_00001g6u	Download File View File

CRYSTAL STRUCTURE OF A DOMAIN SWAPPED DIMER

Ogihara, N.L., Ghirlanda, G., Bryson, J.W., Gingery, M., DeGrado, W.F., Eisenberg, D.

(2001) Proc Natl Acad Sci U S A 98: 1404-1409

Released	2001-02-21
Method	X-RAY DIFFRACTION 1.48 Å
Macromolecule	DOMAIN SWAPPED DIMER (protein)
Unique Ligands	SO4, TFA

Explore in 3D

1HQJ \| pdb_00001hqj	Download File View File

CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE

Burkhard, P., Meier, M., Lustig, A.

(2000) Protein Sci 9: 2294-2301

Released	2001-03-14
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	synthetic construct
Macromolecule	ZJU-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2 (protein)
Unique Ligands	PB, SO4

Explore in 3D

1IC9 \| pdb_00001ic9	Download File View File

NMR SOLUTION STRUCTURE OF THE DESIGNED BETA-SHEET MINI-PROTEIN TH10AOX

Ottesen, J.J., Imperiali, B.

(2001) Nat Struct Biol 8: 535-539

Released	2001-04-11
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	TH10AOX (protein)

Explore in 3D

1ICL \| pdb_00001icl	Download File View File

SOLUTION STRUCTURE OF DESIGNED BETA-SHEET MINI-PROTEIN TH1OX

Ottesen, J.J., Imperiali, B.

(2001) Nat Struct Biol 8: 535-539

Released	2001-04-11
Method	SOLUTION NMR
Macromolecule	TH1OX (protein)

Explore in 3D

1ICO \| pdb_00001ico	Download File View File

SOLUTION STRUCTURE OF DESIGNED BETA-SHEET MINI-PROTEIN TH10BOX

Ottesen, J.J., Imperiali, B.

(2001) Nat Struct Biol 8: 535-539

Released	2001-04-11
Method	SOLUTION NMR
Macromolecule	TH10BOX (protein)

Explore in 3D

1IHQ \| pdb_00001ihq	Download File View File

GLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF A RAT SHORT ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BY EXON 1B

Greenfield, N.J., Yuang, Y.J., Palm, T., Swapna, G.V., Monleon, D., Montelione, G.T., Hitchcock-Degregori, S.E., Northeast Structural Genomics Consortium (NESG)

(2001) J Mol Biology 312: 833-847

Released	2001-10-03
Method	SOLUTION NMR
Organisms	Rattus norvegicus Saccharomyces cerevisiae
Macromolecule	CHIMERIC PEPTIDE GlyTM1bZip: TROPOMYOSIN ALPHA CHAIN, BRAIN-3 and GENERAL CONTROL PROTEIN GCN4 (protein)

Explore in 3D

1J4M \| pdb_00001j4m	Download File View File

Minimized average structure of the 14-residue peptide RG-KWTY-NG-ITYE-GR (MBH12)

Pastor, M.T., Lopez de la Paz, M., Lacroix, E., Serrano, L., Perez-Paya, E.

(2002) Proc Natl Acad Sci U S A 99: 614-619

Released	2001-10-17
Method	SOLUTION NMR
Macromolecule	MBH12 (protein)

Explore in 3D

1JM0 \| pdb_00001jm0	Download File View File

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL

Di Costanzo, L., Geremia, S.

(2001) J Am Chem Soc 123: 12749-12757

Released	2002-01-16
Method	X-RAY DIFFRACTION 1.7 Å
Macromolecule	PROTEIN (FOUR-HELIX BUNDLE MODEL) (protein)
Unique Ligands	DMS, MN

Explore in 3D

1JMB \| pdb_00001jmb	Download File View File

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL

Di Costanzo, L., Geremia, S.

(2001) J Am Chem Soc 123: 12749-12757

Released	2002-01-16
Method	X-RAY DIFFRACTION 2.2 Å
Macromolecule	PROTEIN (FOUR-HELIX BUNDLE MODEL) (protein)
Unique Ligands	DMS, MN

Explore in 3D

1JY4 \| pdb_00001jy4	Download File View File

B4DIMER: A DE NOVO DESIGNED EIGHT-STRANDED BETA-SHEET ASSEMBLED USING A DISULFIDE BOND

Venkatraman, J., Nagana Gowda, G.A., Balaram, P.

(2002) J Am Chem Soc 124: 4987-4994

Released	2002-06-12
Method	SOLUTION NMR
Macromolecule	B4DIMER (protein)

Explore in 3D

1JY6 \| pdb_00001jy6	Download File View File

B4DIMERA: A DE NOVO DESIGNED FOUR-STRANDED BETA-SHEET ASSEMBLED USING A DISULFIDE BOND

Venkatraman, J., Nagana Gowda, G.A., Balaram, P.

(2002) J Am Chem Soc 124: 4987-4994

Released	2002-06-12
Method	SOLUTION NMR
Macromolecule	B4DIMER (protein)

Explore in 3D

1JY9 \| pdb_00001jy9	Download File View File

MINIMIZED AVERAGE STRUCTURE OF DP-TT2

Stanger, H.E., Syud, F.A., Espinosa, J.F., Giriat, I., Muir, T., Gellman, S.H.

(2001) Proc Natl Acad Sci U S A 98: 12015-12020

Released	2001-09-19
Method	SOLUTION NMR
Macromolecule	DP-TT2 (protein)

Explore in 3D

1K09 \| pdb_00001k09	Download File View File

Solution structure of BetaCore, A Designed Water Soluble Four-Stranded Antiparallel b-sheet Protein

Carulla, N., Woodward, C., Barany, G.

(2002) Protein Sci 11: 1539-1551

Released	2002-07-10
Method	SOLUTION NMR
Organisms	Bos taurus
Macromolecule	Core Module I (protein) Core Module II (protein)
Unique Ligands	C55

Explore in 3D

1K43 \| pdb_00001k43	Download File View File

10 Structure Ensemble of the 14-residue peptide RG-KWTY-NG-ITYE-GR (MBH12)

Pastor, M.T., Lopez de la Paz, M., Lacroix, E., Serrano, L., Perez-Paya, E.

(2002) Proc Natl Acad Sci U S A 99: 614-619

Released	2001-10-17
Method	SOLUTION NMR
Macromolecule	MBH12 (protein)

Explore in 3D

1KD8 \| pdb_00001kd8	Download File View File

X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L

Keating, A.E., Malashkevich, V.N., Tidor, B., Kim, P.S.

(2001) Proc Natl Acad Sci U S A 98: 14825-14830

Released	2001-11-28
Method	X-RAY DIFFRACTION 1.9 Å
Macromolecule	GCN4 ACID BASE HETERODIMER ACID-d12Ia16V (protein) GCN4 ACID BASE HETERODIMER BASE-d12La16L (protein)

1 to 25 of 1,696 Structures

Page 1 of 68

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.

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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1BYZ | pdb_00001byz

1C3T | pdb_00001c3t

1CQ0 | pdb_00001cq0

1D7T | pdb_00001d7t

1DJF | pdb_00001djf

1DN3 | pdb_00001dn3

1DNG | pdb_00001dng

1E0M | pdb_00001e0m

1EC5 | pdb_00001ec5

1FME | pdb_00001fme

1G6U | pdb_00001g6u

1HQJ | pdb_00001hqj

1IC9 | pdb_00001ic9

1ICL | pdb_00001icl

1ICO | pdb_00001ico

1IHQ | pdb_00001ihq

1J4M | pdb_00001j4m

1JM0 | pdb_00001jm0

1JMB | pdb_00001jmb

1JY4 | pdb_00001jy4

1JY6 | pdb_00001jy6

1JY9 | pdb_00001jy9

1K09 | pdb_00001k09

1K43 | pdb_00001k43

1KD8 | pdb_00001kd8