5M1Y
  • Download 5m1y
  • View 5m1y
Molmil generated image of 5m1y
THE CASE OF 1LKR HELD AT THE PDB AND ITS VARIABLE AMINO ACID OCCUPANCIES; RE REFINEMENT OF 4OW9 TO CORRECT THIS
Descriptor:Lysozyme C, PLATINUM (II) ION, IODIDE ION, ...
Authors:Helliwell, J.R.
Deposit date:2016-10-11
Release date:2016-10-26
Last modified:2017-09-13
Method:X-RAY DIFFRACTION (1.904 Å)
Cite:The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement of 4ow9 to correct this
Zenodo, 2016
1S3O
  • Download 1s3o
  • View 1s3o
Molmil generated image of 1s3o
HUMAN MITOCHONDRIAL SINGLE STRAND DNA BINDING PROTEIN (HMSSB)
Descriptor:Single-stranded DNA-binding protein, mitochondrial
Authors:Venclovas, C., Ginalski, K., Kang, C.
Deposit date:2004-01-13
Release date:2004-06-22
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.47 Å)
Cite:Sequence-structure mapping errors in the PDB: OB-fold domains
Protein Sci., 13, 2004
4B6Z
  • Download 4b6z
  • View 4b6z
Molmil generated image of 4b6z
CRYSTAL STRUCTURE OF METALLO-CARBOXYPEPTIDASE FROM BURKHOLDERIA CENOCEPACIA
Descriptor:FAMILY M14 UNASSIGNED PEPTIDASE, ZINC ION, GLYCEROL, ...
Authors:Rimsa, V., Eadsforth, T.C., Joosten, R.P., Hunter, W.N.
Deposit date:2012-08-16
Release date:2013-03-27
Last modified:2014-02-26
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:High-Resolution Structure of the M14-Type Cytosolic Carboxypeptidase from Burkholderia Cenocepacia Refined Exploiting Pdb_Redo Strategies.
Acta Crystallogr.,Sect.D, 70, 2014
6DBZ
  • Download 6dbz
  • View 6dbz
Molmil generated image of 6dbz
CRYSTAL STRUCTURE OF NUDIX 1 FROM ARABIDOPSIS THALIANA COMPLEXED WITH ISOPENTENYL DIPHOSPHATE
Descriptor:Nudix hydrolase 1, ISOPENTYL PYROPHOSPHATE, MAGNESIUM ION
Authors:Noel, J.P., Thomas, S.T., Dudareva, N., Henry, L.K.
Deposit date:2018-05-03
Release date:2018-09-19
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Contribution of isopentenyl phosphate to plant terpenoid metabolism.
Nat Plants, 4, 2018
3IZ0
  • Download 3iz0
  • View 3iz0
Molmil generated image of 3iz0
HUMAN NDC80 BONSAI DECORATED MICROTUBULE
Descriptor:alpha tubulin, Chain A from PDB 1JFF, beta tubulin, ...
Authors:Alushin, G.M., Ramey, V.H., Pasqualato, S., Ball, D.A., Grigorieff, N., Musacchio, A., Nogales, E.
Deposit date:2010-08-09
Release date:2010-10-13
Last modified:2018-07-18
Method:ELECTRON MICROSCOPY (8.6 Å)
Cite:The Ndc80 kinetochore complex forms oligomeric arrays along microtubules.
Nature, 467, 2010
3K3E
  • Download 3k3e
  • View 3k3e
Molmil generated image of 3k3e
CRYSTAL STRUCTURE OF THE PDE9A CATALYTIC DOMAIN IN COMPLEX WITH (R)-BAY73-6691
Descriptor:High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, ZINC ION, MAGNESIUM ION, ...
Authors:Wang, H., Luo, X., Ye, M., Hou, J., Robinson, H., Ke, H.
Deposit date:2009-10-02
Release date:2010-02-16
Last modified:2013-11-13
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Insight into Binding of Phosphodiesterase-9A Selective Inhibitors by Crystal Structures and Mutagenesis
J.Med.Chem., 53, 2010
3QI3
  • Download 3qi3
  • View 3qi3
Molmil generated image of 3qi3
CRYSTAL STRUCTURE OF PDE9A(Q453E) IN COMPLEX WITH INHIBITOR BAY73-6691
Descriptor:High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, 1-(2-chlorophenyl)-6-[(2R)-3,3,3-trifluoro-2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one, ZINC ION, ...
Authors:Hou, J., Xu, J., Liu, M., Zhao, R., Lou, H., Ke, H.
Deposit date:2011-01-26
Release date:2011-04-27
Last modified:2014-02-19
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structural asymmetry of phosphodiesterase-9, potential protonation of a glutamic Acid, and role of the invariant glutamine.
Plos One, 6, 2011
4EXO
  • Download 4exo
  • View 4exo
Molmil generated image of 4exo
REVISED, REREFINED CRYSTAL STRUCTURE OF PDB ENTRY 2QHK, METHYL ACCEPTING CHEMOTAXIS PROTEIN
Descriptor:Methyl-accepting chemotaxis protein, PYRUVIC ACID
Authors:Sweeney, E.G., Henderson, J.N., Goers, J., Wreden, C., Hicks, K.G., Foster, J.K., Parthasarathy, R., Remington, S.J., Guillemin, K.
Deposit date:2012-04-30
Release date:2012-05-30
Last modified:2017-11-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure and Proposed Mechanism for the pH-Sensing Helicobacter pylori Chemoreceptor TlpB.
Structure, 20, 2012
6BYO
  • Download 6byo
  • View 6byo
Molmil generated image of 6byo
RESIDUE ASSIGNMENT CORRECTION TO THE VOLTAGE GATED CALCIUM CAV1.1 RABBIT ALPHA 1 SUBUNIT PDB ENTRIES 3JBR & 5GJV
Descriptor:Voltage-dependent L-type calcium channel subunit alpha-1S
Authors:Cardozo, T.J., Martinez-Ortiz, W.
Deposit date:2017-12-21
Release date:2018-05-02
Last modified:2018-05-16
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:An Improved Method for Modeling Voltage-Gated Ion Channels at Atomic Accuracy Applied to Human CavChannels.
Cell Rep, 23, 2018
2IBL
  • Download 2ibl
  • View 2ibl
Molmil generated image of 2ibl
CRYSTAL STRUCTURE OF A HELPER MOLECULE (HT-MF-THROMB) BASED ON MINI-FIBRITIN (MF) CRYSTAL STRUCTURE (PDB:1OX3).
Descriptor:Fibritin
Authors:Boudko, S.P., Rossmann, M.G.
Deposit date:2006-09-11
Release date:2007-02-27
Last modified:2017-06-14
Method:X-RAY DIFFRACTION (1.32 Å)
Cite:The Coiled-coil Domain Structure of the Sin Nombre Virus Nucleocapsid Protein.
J.Mol.Biol., 366, 2007
3URP
  • Download 3urp
  • View 3urp
Molmil generated image of 3urp
RE-REFINEMENT OF PDB ENTRY 5RNT - RIBONUCLEASE T1 WITH GUANOSINE-3',5'-DIPHOSPHATE AND PHOSPHATE ION BOUND
Descriptor:Guanyl-specific ribonuclease T1, GUANOSINE-3',5'-DIPHOSPHATE, PHOSPHATE ION, ...
Authors:Smart, O.S., Womack, T.O., Flensburg, C., Keller, P., Sharff, A., Paciorek, W., Vonrhein, C., Bricogne, G.
Deposit date:2011-11-22
Release date:2012-03-28
Last modified:2013-02-20
Method:X-RAY DIFFRACTION (3.19 Å)
Cite:Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.
Acta Crystallogr.,Sect.D, 68, 2012
5OQ1
  • Download 5oq1
  • View 5oq1
Molmil generated image of 5oq1
CRYSTAL STRUCTURE OF SERRATIA MARCESCENS CHIX (USED AS MR MODEL FOR SUPERIOR PDB 5OPZ)
Descriptor:ChiX, ZINC ION, CHLORIDE ION
Authors:Owen, R.A., Fyfe, P.K., Lodge, A., Biboy, J., Vollmer, W., Hunter, W.N., Sargent, F.
Deposit date:2017-08-10
Release date:2018-01-17
Last modified:2018-02-07
Method:X-RAY DIFFRACTION (1.34 Å)
Cite:Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens.
Biochem. J., 475, 2018
5UMO
  • Download 5umo
  • View 5umo
Molmil generated image of 5umo
STRUCTURE OF EXTRACELLULAR SIGNAL-REGULATED KINASE
Descriptor:Mitogen-activated protein kinase 1, SULFATE ION
Authors:CHLEBOWICZ, J., ZHANG, F., GOLDSMITH, E.J.
Deposit date:2017-01-27
Release date:2017-03-01
Last modified:2018-03-07
Method:X-RAY DIFFRACTION (2.26 Å)
Cite:Atomic structure of the MAP kinase ERK2 at 2.3 A resolution.
Nature, 367, 1994
5VEH
  • Download 5veh
  • View 5veh
Molmil generated image of 5veh
RE-REFINEMENT OF THE PDB STRUCTURE 1YIZ OF AEDES AEGYPTI KYNURENINE AMINOTRANSFERASE
Descriptor:Kynurenine aminotransferase, BROMIDE ION, GLYCEROL
Authors:Wlodawer, A., Dauter, Z., Minor, W., Stanfield, R., Porebski, P., Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B.
Deposit date:2017-04-04
Release date:2017-11-29
Last modified:2018-04-18
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Detect, correct, retract: How to manage incorrect structural models.
FEBS J., 285, 2018
5VEP
  • Download 5vep
  • View 5vep
Molmil generated image of 5vep
MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2F
Descriptor:Kynurenine--oxoglutarate transaminase 3, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DI(HYDROXYETHYL)ETHER, ...
Authors:Wlodawer, A., Dauter, Z., Minor, W., Stanfield, R., Porebski, P., Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B.
Deposit date:2017-04-05
Release date:2017-11-29
Last modified:2018-02-14
Method:X-RAY DIFFRACTION (2.59 Å)
Cite:Detect, correct, retract: How to manage incorrect structural models.
FEBS J., 285, 2018
5VEQ
  • Download 5veq
  • View 5veq
Molmil generated image of 5veq
MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Y
Descriptor:Kynurenine--oxoglutarate transaminase 3, 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ...
Authors:Wlodawer, A., Dauter, Z., Minor, W., Stanfield, R., Porebski, P., Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B.
Deposit date:2017-04-05
Release date:2017-11-29
Last modified:2018-02-14
Method:X-RAY DIFFRACTION (2.26 Å)
Cite:Detect, correct, retract: How to manage incorrect structural models.
FEBS J., 285, 2018
5VER
  • Download 5ver
  • View 5ver
Molmil generated image of 5ver
MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Z
Descriptor:Kynurenine--oxoglutarate transaminase 3, PYRIDOXAL-5'-PHOSPHATE, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ...
Authors:Wlodawer, A., Dauter, Z., Minor, W., Stanfield, R., Porebski, P., Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B.
Deposit date:2017-04-05
Release date:2017-11-29
Last modified:2018-02-14
Method:X-RAY DIFFRACTION (2.81 Å)
Cite:Detect, correct, retract: How to manage incorrect structural models.
FEBS J., 285, 2018
5VET
  • Download 5vet
  • View 5vet
Molmil generated image of 5vet
PHOSPHOLIPASE A2, RE-REFINEMENT OF THE PDB STRUCTURE 1JQ8 WITHOUT THE PUTATIVE COMPLEXED OLIGOPEPTIDE
Descriptor:Phospholipase A2 VRV-PL-VIIIa
Authors:Wlodawer, A., Dauter, Z., Minor, W., Stanfield, R., Porebski, P., Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B.
Deposit date:2017-04-05
Release date:2018-06-20
Method:X-RAY DIFFRACTION (2 Å)
Cite:Detect, correct, retract: How to manage incorrect structural models.
FEBS J., 285, 2018
5WFN
  • Download 5wfn
  • View 5wfn
Molmil generated image of 5wfn
REVISED MODEL OF LEIOMODIN 2-MEDIATED ACTIN REGULATION (ALTERNATE REFINEMENT OF PDB 4RWT)
Descriptor:Actin-5C, Leiomodin-2, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ...
Authors:Yurtsever, Z., Eck, M.J., Dominguez, R.
Deposit date:2017-07-12
Release date:2017-08-30
Last modified:2018-08-22
Method:X-RAY DIFFRACTION (3 Å)
Cite:Crystal structure of leiomodin 2 in complex with actin: a structural and functional reexamination
Biophys.J., 113, 2017
6B90
  • Download 6b90
  • View 6b90
Molmil generated image of 6b90
MULTICONFORMER MODEL OF APO WT PTP1B WITH GLYCEROL AT 100 K (ALTERNATIVE REFINEMENT OF PDB 1SUG SHOWING CONFORMATIONAL HETEROGENEITY)
Descriptor:Tyrosine-protein phosphatase non-receptor type 1, GLYCEROL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Authors:Keedy, D.A., Hill, Z.B., Biel, J.T., Kang, E., Rettenmaier, T.J., Brandao-Neto, J., von Delft, F., Wells, J.A., Fraser, J.S.
Deposit date:2017-10-09
Release date:2018-06-20
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.
Elife, 7, 2018
3FIB
  • Download 3fib
  • View 3fib
Molmil generated image of 3fib
RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0: A FURTHER REFINEMENT OF PDB ENTRY 1FIB, AND DIFFERS FROM 1FIB BY THE MODELLING OF A CIS PEPTIDE BOND BETWEEN RESIDUES K338 AND C339
Descriptor:FIBRINOGEN GAMMA CHAIN RESIDUES, CALCIUM ION
Authors:Pratt, K.P., Cote, H.C.F., Chung, D.W., Stenkamp, R.E., Davie, E.W.
Deposit date:1997-07-14
Release date:1997-09-17
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro.
Proc.Natl.Acad.Sci.USA, 94, 1997
3QL3
  • Download 3ql3
  • View 3ql3
Molmil generated image of 3ql3
RE-REFINED COORDINATES FOR PDB ENTRY 1RX2
Descriptor:Dihydrofolate reductase, FOLIC ACID, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ...
Authors:Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.
Deposit date:2011-02-02
Release date:2011-04-27
Last modified:2014-11-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.
Science, 332, 2011
3SYU
  • Download 3syu
  • View 3syu
Molmil generated image of 3syu
RE-REFINED COORDINATES FOR PDB ENTRY 1DET - RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP
Descriptor:Guanyl-specific ribonuclease T1, SODIUM ION, GUANOSINE-2'-MONOPHOSPHATE, ...
Authors:Smart, O.S., Womack, T.O., Bricogne, G.
Deposit date:2011-07-18
Release date:2012-03-28
Last modified:2012-05-02
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.
Acta Crystallogr.,Sect.D, 68, 2012
3V56
  • Download 3v56
  • View 3v56
Molmil generated image of 3v56
RE-REFINEMENT OF PDB ENTRY 1OSG - COMPLEX BETWEEN BAFF AND A BR3 DERIVED PEPTIDE PRESENTED IN A BETA-HAIRPIN SCAFFOLD - REVEALS AN ADDITONAL COPY OF THE PEPTIDE.
Descriptor:Tumor necrosis factor ligand superfamily member 13B, BR3 derived peptive, SULFATE ION
Authors:Smart, O.S., Womack, T.O., Flensburg, C., Keller, P., Sharff, A., Paciorek, W., Vonrhein, C., Bricogne, G.
Deposit date:2011-12-16
Release date:2012-03-28
Last modified:2018-01-24
Method:X-RAY DIFFRACTION (3 Å)
Cite:Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.
Acta Crystallogr.,Sect.D, 68, 2012
4E1B
  • Download 4e1b
  • View 4e1b
Molmil generated image of 4e1b
RE-REFINEMENT OF PDB ENTRY 2EQA - SUA5 PROTEIN FROM SULFOLOBUS TOKODAII WITH BOUND THREONYLCARBAMOYLADENYLATE
Descriptor:YrdC/Sua5 family protein, MAGNESIUM ION, threonylcarbamoyladenylate
Authors:Parthier, C., Goerlich, S., Jaenecke, F., Breithaupt, C., Braeuer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Boettcher, C., Scheel, D., Stubbs, M.T.
Deposit date:2012-03-06
Release date:2012-03-14
Last modified:2012-05-02
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.
Angew.Chem.Int.Ed.Engl., 51, 2012
PDBj@FacebookPDBj@TwitterwwPDBwwPDB Foundation

Copyright © 2013-2019 Protein Data Bank Japan