Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
Search by PDB author
7UNJ
DownloadVisualize
BU of 7unj by Molmil
De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester matching geometry of purple bacterial special pair, SP1-ZnPPaM
Descriptor: 1,2-ETHANEDIOL, SP1-ZnPPaM designed chlorophyll dimer protein, SULFATE ION, ...
Authors:Kennedy, M.A, Stoddard, B.L, Ennist, N.M.
Deposit date:2022-04-11
Release date:2023-04-19
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (2 Å)
Cite:De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
7UNH
DownloadVisualize
BU of 7unh by Molmil
De novo designed chlorophyll dimer protein in apo state, SP2
Descriptor: 1,2-ETHANEDIOL, SP2 designed chlorophyll dimer protein
Authors:Kennedy, M.A, Stoddard, B.L, Ennist, N.M.
Deposit date:2022-04-11
Release date:2023-04-19
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
7UNI
DownloadVisualize
BU of 7uni by Molmil
De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM
Descriptor: 1,2-ETHANEDIOL, PHOSPHATE ION, SP2-ZnPPaM designed chlorophyll dimer protein, ...
Authors:Kennedy, M.A, Stoddard, B.L, Ennist, N.M.
Deposit date:2022-04-11
Release date:2023-04-19
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
1MOW
DownloadVisualize
BU of 1mow by Molmil
E-DreI
Descriptor: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3', GLYCEROL, ...
Authors:Chevalier, B.S, Kortemme, T, Chadsey, M.S, Baker, D, Monnat Jr, R.J, Stoddard, B.L.
Deposit date:2002-09-10
Release date:2002-11-29
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Design, Activity and Structure of a Highly Specific Artificial Endonuclease
Mol.Cell, 10, 2002
5JSB
DownloadVisualize
BU of 5jsb by Molmil
Crystal structure of Mcl1-inhibitor complex
Descriptor: Induced myeloid leukemia cell differentiation protein Mcl-1, Mcl-1 inhibitor
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2016-05-07
Release date:2016-11-16
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.74 Å)
Cite:Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer.
Elife, 5, 2016
1N3F
DownloadVisualize
BU of 1n3f by Molmil
Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence)
Descriptor: 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3'), CALCIUM ION, ...
Authors:Chevalier, B, Turmel, M, Lemieux, C, Monnat, R.J, Stoddard, B.L.
Deposit date:2002-10-28
Release date:2003-06-03
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI
J.Mol.Biol., 329, 2003
1N3E
DownloadVisualize
BU of 1n3e by Molmil
Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence)
Descriptor: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3', 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3', CALCIUM ION, ...
Authors:Chevalier, B, Turmel, M, Lemieux, C, Monnat, R.J, Stoddard, B.L.
Deposit date:2002-10-28
Release date:2003-06-03
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI
J.Mol.Biol., 329, 2003
5JSN
DownloadVisualize
BU of 5jsn by Molmil
Bcl2-inhibitor complex
Descriptor: Apoptosis regulator Bcl-2, Bcl2 inhibitor
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2016-05-09
Release date:2016-11-16
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer.
Elife, 5, 2016
6EG7
DownloadVisualize
BU of 6eg7 by Molmil
BbvCI B2 dimer with I3C clusters
Descriptor: 1,2-ETHANEDIOL, 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid, BbvCI endonuclease subunit 2, ...
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2018-08-19
Release date:2018-11-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.
Nucleic Acids Res., 47, 2019
5TH3
DownloadVisualize
BU of 5th3 by Molmil
Restriction/modification system-Type II R.SwaI cleaved DNA complex
Descriptor: 1,2-ETHANEDIOL, ACETATE ION, DNA (cleaved 25-MER, ...
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2016-09-29
Release date:2016-12-21
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.
Nucleic Acids Res., 45, 2017
7LVV
DownloadVisualize
BU of 7lvv by Molmil
cryoEM structure DrdV-DNA complex
Descriptor: CALCIUM ION, DNA (27-MER), DNA (28-MER), ...
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2021-02-26
Release date:2021-03-17
Last modified:2024-03-06
Method:ELECTRON MICROSCOPY (3.25 Å)
Cite:Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM.
Structure, 29, 2021
7LO5
DownloadVisualize
BU of 7lo5 by Molmil
cryoEM structure DrdV-DNA complex
Descriptor: CALCIUM ION, DNA (27-MER), DNA (28-MER), ...
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2021-02-09
Release date:2021-03-17
Last modified:2024-03-06
Method:ELECTRON MICROSCOPY (2.86 Å)
Cite:Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM.
Structure, 29, 2021
3KO2
DownloadVisualize
BU of 3ko2 by Molmil
I-MsoI re-designed for altered DNA cleavage specificity (-7C)
Descriptor: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', CALCIUM ION, ...
Authors:Taylor, G.K, Stoddard, B.L.
Deposit date:2009-11-13
Release date:2010-05-19
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Nucleic Acids Res., 38, 2010
3LDY
DownloadVisualize
BU of 3ldy by Molmil
An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI
Descriptor: CALCIUM ION, DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3'), DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3'), ...
Authors:Shen, B.W, Heiter, D, Chan, S.-H, Xu, S.-Y, Wilson, G, Stoddard, B.L.
Deposit date:2010-01-13
Release date:2010-04-21
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
Structure, 18, 2010
2ERH
DownloadVisualize
BU of 2erh by Molmil
Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7 DNAse and the Im7 immunity protein
Descriptor: Colicin E7, Colicin E7 immunity protein
Authors:Joachimiak, L.A, Kortemme, T, Stoddard, B.L, Baker, D.
Deposit date:2005-10-24
Release date:2006-07-25
Last modified:2023-08-23
Method:X-RAY DIFFRACTION (2 Å)
Cite:Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein-Protein Interface.
J.Mol.Biol., 361, 2006
2EX5
DownloadVisualize
BU of 2ex5 by Molmil
Group I Intron-encoded Homing Endonuclease I-CeuI Complexed With DNA
Descriptor: CALCIUM ION, DNA endonuclease I-CeuI, I-CeuI DNA target site, ...
Authors:Spiegel, P.C, Stoddard, B.L.
Deposit date:2005-11-07
Release date:2006-05-23
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold.
Structure, 14, 2006
2FLD
DownloadVisualize
BU of 2fld by Molmil
I-MsoI Re-Designed for Altered DNA Cleavage Specificity
Descriptor: 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*TP*TP*CP*CP*G)-3', CALCIUM ION, ...
Authors:Ashworth, J, Duarte, C.M, Havranek, J.J, Sussman, D, Monnat, R.J, Stoddard, B.L, Baker, D.
Deposit date:2006-01-05
Release date:2006-06-06
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2 Å)
Cite:Computational redesign of endonuclease DNA binding and cleavage specificity.
Nature, 441, 2006
8ETQ
DownloadVisualize
BU of 8etq by Molmil
Designed pentafoil knot protein folded into a trefoil knot
Descriptor: k-cTRP5
Authors:Doyle, L.A, Kibler, R.D, Bradley, P, Stoddard, B.L.
Deposit date:2022-10-17
Release date:2023-10-25
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.42 Å)
Cite:De novo design of knotted tandem repeat proteins.
Nat Commun, 14, 2023
8FLX
DownloadVisualize
BU of 8flx by Molmil
De novo designed homotrimer; the fusion product of BGL17 and DHR59
Descriptor: LK031
Authors:Kibler, R.D, Kennedy, M.A, Stoddard, B.L, Lee, S.
Deposit date:2022-12-22
Release date:2023-06-28
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (4.5 Å)
Cite:De novo designed homotrimer; the fusion product of BGL17 and DHR59
To Be Published
1YSB
DownloadVisualize
BU of 1ysb by Molmil
Yeast Cytosine Deaminase Triple Mutant
Descriptor: CALCIUM ION, Cytosine deaminase, ZINC ION
Authors:Korkegian, A, Black, M.E, Baker, D, Stoddard, B.L.
Deposit date:2005-02-08
Release date:2005-05-17
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Computational thermostabilization of an enzyme.
Science, 308, 2005
1YSD
DownloadVisualize
BU of 1ysd by Molmil
Yeast Cytosine Deaminase Double Mutant
Descriptor: CALCIUM ION, Cytosine deaminase, ZINC ION
Authors:Korkegian, A, Black, M.E, Baker, D, Stoddard, B.L.
Deposit date:2005-02-08
Release date:2005-05-17
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Computational thermostabilization of an enzyme.
Science, 308, 2005
299D
DownloadVisualize
BU of 299d by Molmil
CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: THE HAMMERHEAD RIBOZYME
Descriptor: RNA HAMMERHEAD RIBOZYME
Authors:Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A.
Deposit date:1996-12-14
Release date:1997-01-24
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (3 Å)
Cite:Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
1IQD
DownloadVisualize
BU of 1iqd by Molmil
Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab.
Descriptor: HUMAN FACTOR VIII, HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN, HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN
Authors:Spiegel Jr, P.C, Jacquemin, M, Saint-Remy, J.M, Stoddard, B.L, Pratt, K.P.
Deposit date:2001-07-21
Release date:2001-08-15
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII.
Blood, 98, 2001
1G9Y
DownloadVisualize
BU of 1g9y by Molmil
HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM
Descriptor: 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', CALCIUM ION, ...
Authors:Chevalier, B, Monnat, R.J, Stoddard, B.L.
Deposit date:2000-11-28
Release date:2001-04-02
Last modified:2023-08-09
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001
1G9Z
DownloadVisualize
BU of 1g9z by Molmil
LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM
Descriptor: 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', ...
Authors:Chevalier, B, Monnat, R.J, Stoddard, B.L.
Deposit date:2000-11-28
Release date:2001-04-02
Last modified:2023-08-09
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.
Nat.Struct.Biol., 8, 2001

221051

건을2024-06-12부터공개중

PDB statisticsPDBj update infoContact PDBjnumon