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 = "Komander, D."

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 146 Structures.

Refinements

Structure Determination Methodology

experimental (146)

Scientific Name of Source Organism

	Homo sapiens (113)
	Pediculus humanus corporis (10)
	Serratia marcescens (10)
	Bos taurus (4)
	Crimean-Congo hemorrhagic fever virus strain IbAr10200 (4)
	Severe acute respiratory syndrome coronavirus 2 (4)
	Mus musculus (3)
	synthetic construct (3)
	Chlamydia trachomatis (2)
	Salmonella enterica (2)

More...

Taxonomy

	Eukaryota (125)
	Bacteria (23)
	Riboviria (9)
	other sequences (3)

Experimental Method

	X-RAY DIFFRACTION (133)
	ELECTRON MICROSCOPY (10)
	SOLUTION NMR (3)

Polymer Entity Type

Protein (146)

Refinement Resolution (Å)

	1.0 - 1.5 (13)
	1.5 - 2.0 (41)
	2.0 - 2.5 (42)
	2.5 - 3.0 (28)
	3.0 - 3.5 (15)
	3.5 - 4.0 (4)

Release Date

	2000 - 2004 (23)
	2005 - 2009 (19)
	2010 - 2014 (26)
	2015 - 2019 (50)
	2020 - 2024 (25)
	2025 - 2029 (3)

Enzyme Classification Name

	Hydrolases (61)
	Transferases (55)
	Ligases (11)

Membrane Protein Annotation

	PDBTM (3)
	OPM (2)

Symmetry Type

	Asymmetric (109)
	Cyclic (35)
	Dihedral (5)

SCOP Classification

	Alpha and beta proteins (a+b) (65)
	All beta proteins (19)
	Artifacts (14)
	Alpha and beta proteins (a/b) (10)
	All alpha proteins (1)

AllSelected

1 to 25 of 146 Structures

Page 1 of 6

Sort by

Explore in 3D

1E6N \| pdb_00001e6n	Download File View File

Chitinase B from Serratia marcescens inactive mutant E144Q in complex with N-acetylglucosamine-pentamer

Komander, D., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2001) Proc Natl Acad Sci U S A 98: 8979

Released	2001-06-22
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	NAG

Explore in 3D

1E6P \| pdb_00001e6p	Download File View File

Chitinase B from Serratia marcescens inactive mutant E144Q

Komander, D., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2001) Proc Natl Acad Sci U S A 98: 8979

Released	2001-06-22
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	GOL, SO4

Explore in 3D

1E6R \| pdb_00001e6r	Download File View File

Chitinase B from Serratia marcescens wildtype in complex with inhibitor allosamidin

Komander, D., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2001) Proc Natl Acad Sci U S A 98: 8979

Released	2001-06-22
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	AMI, SO4
Unique branched monosaccharides	NAA

Explore in 3D

1E6Z \| pdb_00001e6z	Download File View File

CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH CATALYTIC INTERMEDIATE

Komander, D., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2001) Proc Natl Acad Sci U S A 98: 8979

Released	2001-06-22
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	NAG, NGO, SO4
Unique branched monosaccharides	NAG

Explore in 3D

1GOI \| pdb_00001goi	Download File View File

Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 A resolution

Kolstad, G., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2002) Acta Crystallogr D Biol Crystallogr 58: 377

Released	2001-11-15
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	GOL, SO4

Explore in 3D

1GPF \| pdb_00001gpf	Download File View File

CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PSAMMAPLIN

Komander, D., Van Aalten, D.M.

(2002) Bioorg Med Chem 10: 1123

Released	2002-10-31
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	SO4

Explore in 3D

1H1W \| pdb_00001h1w	Download File View File

High resolution crystal structure of the human PDK1 catalytic domain

Biondi, R.M., Komander, D., Thomas, C.C., Lizcano, J.M., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

(2003) EMBO J 21: 4219

Released	2003-07-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	ATP, GOL, SO4

Explore in 3D

1OGB \| pdb_00001ogb	Download File View File

Chitinase b from Serratia marcescens mutant D142N

Vaaje-Kolstad, G., Houston, D.R., Rao, F.V., Peter, M.G., Synstad, B., van Aalten, D.M.F., Eijsink, V.G.H.

(2004) Biochim Biophys Acta 1696: 103-111

Released	2004-04-27
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	GOL, SO4

Explore in 3D

1OGG \| pdb_00001ogg	Download File View File

chitinase b from serratia marcescens mutant d142n in complex with inhibitor allosamidin

Vaaje-Kolstad, G., Houston, D.R., Rao, F.V., Peter, M.G., Synstad, B., van Aalten, D.M.F., Eijsink, V.G.H.

(2004) Biochim Biophys Acta 1696: 103-111

Released	2004-04-27
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	AMI, GOL, SO4
Unique branched monosaccharides	NAA

Explore in 3D

1OKY \| pdb_00001oky	Download File View File

Structure of human PDK1 kinase domain in complex with staurosporine

Komander, D., Kular, G.S., Alessi, D.R., Van Aalten, D.M.F.

(2003) Biochem J 375: 255

Released	2004-07-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 (protein)
Unique Ligands	GOL, SO4, STU

Explore in 3D

1OKZ \| pdb_00001okz	Download File View File

Structure of human PDK1 kinase domain in complex with UCN-01

Komander, D., Kular, G.S., Alessi, D.R., Van Aalten, D.M.F.

(2003) Biochem J 375: 255

Released	2004-07-29
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 (protein)
Unique Ligands	GOL, SO4, UCN

Explore in 3D

1UPQ \| pdb_00001upq	Download File View File

Crystal structure of the pleckstrin homology (PH) domain of PEPP1

Milburn, C.C., Komander, D., Deak, M., Alessi, D.R., van Aalten, D.M.F.

To be published

Released	2004-10-07
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Homo sapiens
Macromolecule	PEPP1 (protein)
Unique Ligands	SO4

Explore in 3D

1UPR \| pdb_00001upr	Download File View File

Crystal structure of the PEPP1 pleckstrin homology domain in complex with Inositol 1,3,4,5-tetrakisphosphate

Milburn, C.C., Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

To be published

Released	2004-10-20
Method	X-RAY DIFFRACTION 2.27 Å
Organisms	Homo sapiens
Macromolecule	PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY A MEMBER 4 (protein)
Unique Ligands	4IP

Explore in 3D

1UR8 \| pdb_00001ur8	Download File View File

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

Vaaje-Kolstad, G., Vasella, A., Peter, M.G., Netter, C., Houston, D.R., Westereng, B., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2004) J Biological Chem 279: 3612

Released	2004-04-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	GDL, NAG

Explore in 3D

1UR9 \| pdb_00001ur9	Download File View File

Interactions of a family 18 chitinase with the designed inhibitor HM508, and its degradation product, chitobiono-delta-lactone

Vaaje-Kolstad, G., Vasella, A., Peter, M.G., Netter, C., Houston, D.R., Westereng, B., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2004) J Biological Chem 279: 3612

Released	2004-04-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Serratia marcescens
Macromolecule	CHITINASE B (protein)
Unique Ligands	GOL, PHJ, SO4
Unique branched monosaccharides	GDL, NAG

Explore in 3D

1UU3 \| pdb_00001uu3	Download File View File

Structure of human PDK1 kinase domain in complex with LY333531

Komander, D., Kular, G.S., Schuttelkopf, A.W., Deak, M., Prakash, K.R., Bain, J., Elliot, M., Garrido-Franco, M., Kozikowski, A.P., Alessi, D.R., Van Aalten, D.M.F.

(2004) Structure 12: 215

Released	2004-03-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	GOL, LY4, SO4

Explore in 3D

1UU7 \| pdb_00001uu7	Download File View File

Structure of human PDK1 kinase domain in complex with BIM-2

Komander, D., Kular, G.S., Schuttelkopf, A.W., Deak, M., Prakash, K.R., Bain, J., Elliot, M., Garrido-Franco, M., Kozikowski, A.P., Alessi, D.R., Van Aalten, D.M.F.

(2004) Structure 12: 215

Released	2004-03-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	BI2, GOL, SO4

Explore in 3D

1UU8 \| pdb_00001uu8	Download File View File

Structure of human PDK1 kinase domain in complex with BIM-1

Komander, D., Kular, G.S., Schuttelkopf, A.W., Deak, M., Prakash, K.R., Bain, J., Elliot, M., Garrido-Franco, M., Kozikowski, A.P., Alessi, D.R., Van Aalten, D.M.F.

(2004) Structure 12: 215

Released	2004-03-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	BI1, GOL, SO4

Explore in 3D

1UU9 \| pdb_00001uu9	Download File View File

Structure of human PDK1 kinase domain in complex with BIM-3

Komander, D., Kular, G.S., Schuttelkopf, A.W., Deak, M., Prakash, K.R., Bain, J., Elliot, M., Garrido-Franco, M., Kozikowski, A.P., Alessi, D.R., Van Aalten, D.M.F.

(2004) Structure 12: 215

Released	2004-03-04
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Spodoptera frugiperda
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	BI3, GOL, SO4

Explore in 3D

1UVR \| pdb_00001uvr	Download File View File

Structure of human PDK1 kinase domain in complex with BIM-8

Komander, D., Garrido-Franco, M., Kular, G.S., Schuttelkopf, A.W., Deak, M., Prakash, K.R., Bain, J., Elliot, M., Kozikowski, A.P., Alessi, D.R., Van Aalten, D.M.F.

(2004) Structure 12: 215

Released	2004-03-04
Method	X-RAY DIFFRACTION 2.81 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	BI8, GOL, SO4

Explore in 3D

1W1D \| pdb_00001w1d	Download File View File

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate

Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

(2004) EMBO J 23: 3918

Released	2004-11-19
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	4IP, AU, GOL

Explore in 3D

1W1G \| pdb_00001w1g	Download File View File

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate

Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

(2004) EMBO J 23: 3918

Released	2004-11-19
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	4PT

Explore in 3D

1W1H \| pdb_00001w1h	Download File View File

Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain

Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

(2004) EMBO J 23: 3918

Released	2004-11-19
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	GOL, SO4

Explore in 3D

1Z5M \| pdb_00001z5m	Download File View File

Crystal Structure Of N1-[3-[[5-bromo-2-[[3-[(1-pyrrolidinylcarbonyl)amino]phenyl]amino]-4-pyrimidinyl]amino]propyl]-2,2-dimethylpropanediamide Complexed with Human PDK1

Whitlow, M., Adler, M.

(2005) J Biological Chem 280: 19867-19874

Released	2005-04-19
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Homo sapiens
Macromolecule	3-phosphoinositide dependent protein kinase-1 (protein)
Unique Ligands	CL, GOL, LI8, SO4

Explore in 3D

2BIY \| pdb_00002biy	Download File View File

Structure of PDK1-S241A mutant kinase domain

Komander, D., Kular, G.S., Deak, M., Alessi, D.R., van Aalten, D.M.F.

(2005) J Biological Chem 280: 18797-18802

Released	2005-02-23
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 (protein)
Unique Ligands	ATP, GOL, SO4

1 to 25 of 146 Structures

Page 1 of 6

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

1E6N | pdb_00001e6n

1E6P | pdb_00001e6p

1E6R | pdb_00001e6r

1E6Z | pdb_00001e6z

1GOI | pdb_00001goi

1GPF | pdb_00001gpf

1H1W | pdb_00001h1w

1OGB | pdb_00001ogb

1OGG | pdb_00001ogg

1OKY | pdb_00001oky

1OKZ | pdb_00001okz

1UPQ | pdb_00001upq

1UPR | pdb_00001upr

1UR8 | pdb_00001ur8

1UR9 | pdb_00001ur9

1UU3 | pdb_00001uu3

1UU7 | pdb_00001uu7

1UU8 | pdb_00001uu8

1UU9 | pdb_00001uu9

1UVR | pdb_00001uvr

1W1D | pdb_00001w1d

1W1G | pdb_00001w1g

1W1H | pdb_00001w1h

1Z5M | pdb_00001z5m

2BIY | pdb_00002biy