Primary Citation PubMed: 11274458
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Robust structure-based resonance assignment for functional protein studies by NMR.
(2010) J Biomol NMR 46
PubMed: 20024602 | PubMedCentral: PMC2813526 | DOI: 10.1007/s10858-009-9390-3
Experimental data for Lysozyme The H N – H N NOE-data set deposited in the PDB (1E8L) (Schwalbe et al.
Publication Year: 2010
What lessons can be learned from studying the folding of homologous proteins?
(2010) Methods 52
PubMed: 20570731 | PubMedCentral: PMC2965948 | DOI: 10.1016/j.ymeth.2010.06.003
Class (fold) Superfamily Protein (species) Method of investigation PDB code Experimental references Comparative references a All-α (Acyl-CoA binding protein-like) Acyl-CoA binding protein ACBP... (Cow) Φ-Value analysis 2ABD [93,94]  ACBP (Rat) WT kinetics 2ABD b  ACBP (Yeast) Φ-Value analysis 2ABD b 
All-α (Acyl carrier protein-like) Colicin E immunity proteins Im7 ( E. coli ) Φ-Value analysis 1AYI   Im9 ( E. coli ) Φ-Value analysis 1IMQ [29,30,95]
All-α (Cytochrome c ) Cytochrome c Cytochrome c (Horse) Hydrogen exchange 1HRC   Cytochrome c 2 ( R. capsulatus ) WT kinetics 1C2R  Cytochrome c 551 ( P. aeruginosa ) Minimal Φ-value analysis 2PAC  Cytochrome c 552 ( H. thermophilus ) WT kinetics 1AYG  Cytochrome c 552 ( T. thermophilus ) WT kinetics 1C52  Mitochondrial cytochrome c (Yeast) WT kinetics 1YCC 
All-α (Four-helical up-and-down bundle) Cytochromes Cytochrome b 562 ( E. coli ) Hydrogen exchange 1APC  FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) FRB (Human) WT kinetics 1AUE 
All-α (DNA/RNA-binding 3-helical bundle) Homeodomain-like DNA-binding domain of human telomeric protein hTRF1 (Human) WT kinetics 1BA5   En-Hd (Drosophila) Φ-Value analysis 1ENH [7,105] c-Myb DNA-binding domain (Mouse) Φ-Value analysis 1IDY  Rap1 (Human) WT kinetics 1FEX 
All-α (Globin-like) Globin-like Leghemoglobin (Soybean) Hydrogen exchange 1FSL   Myoglobin (Sperm whale) Hydrogen exchange 1A6M 
All-α (peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex) Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex E3 binding domain of dihydrolipoamide acetyltransferase [E3BD] ( B. stearothermophilus ) Φ-Value analysis 1EBD   E3-binding domain of dihydrolipoamide succinyltransferase [BBL] ( E. coli ) Φ-Value analysis 1BBL  POB ( P. aerophilium ) Φ-Value analysis 1BBL b 
All-α (ROP-like) ROP protein ROP ( E. agglomerans ) WT kinetics 1ROP b   ROP ( E. coli ) WT kinetics 1ROP  ROP ( P. vulgaris ) WT kinetics 1ROP b 
All-α (spectrin repeat-like) Spectrin repeat Alpha chain R15 (Chicken) Φ-Value analysis 1U5P   Alpha chain R16 (Chicken) Φ-Value analysis 1CUN  Alpha chain R17 (Chicken) Φ-Value analysis 1CUN 
α/β (α/β knot) α/β knot YbeA ( E. coli ) Φ-Value analysis 1NS5   YibK ( H. influenzae ) Φ-Value analysis 1J85 
α/β (Dihydrofolate reductase-like) Dihydrofolate reductase-like Dihydrofolate reductase ( E. coli ) WT kinetics, Ligand binding 1RA9   Dihyrofolate reductase ( L. casei ) WT kinetics, Ligand binding 3DFR  Dihydrofolate reductase (Human) WT kinetics, Ligand binding 1KMV 
α/β (flavodoxin-like) CheY-like CheY ( E. coli ) Φ-Value analysis 1EAY   Flavoproteins Apoflavodoxin ( A. vinelandii ) WT kinetics 1YOB  Flavodoxin ( Anabaena pcc 7119 ) Φ-Value analysis 1FTG 
α/β (Phosphoglycerate kinase) Phosphoglycerate kinase Phosphoglycerate kinase ( B. stearothermophilus ) Minimal Φ-value analysis 1PHP  Phosphoglycerate kinase (Yeast) WT kinetics 3PGK 
α/β (RNase-H-like Motif) RNase-H-like RNase-H ( E.coli ) Hydrogen exchange Limited mutagenesis 1F21 [168,169] RNase-H ( T. thermophilus ) Hydrogen exchange 1RIL  [170,171] RNase-H ( C. tepidum ) WT kinetics 3H08 
α/β (TIM β/α-barrel) Ribulose-phosphate binding barrel Trptophan synthase α-subunit [αTS] ( E. coli ) WT kinetics 1V7Y   Indole-3-glycerophosphate synthase [sIGPS] ( S. solfataricus ) WT kinetics, Hydrogen exchange 1IGS [118,119]
Xylose isomerase-like IOLI ( B. subtilis ) WT kinetics 1I60 
α + β (Ferredoxin-like) Acyl-phosphatase-like AcP (Human) Φ-Value analysis 1APS b [26,120] [26,65,121] HypF ( E. coli ) WT kinetics 1GXU  Protease propeptides/inhibitors Procarboxy-peptidase A2 (Human) Φ-Value analysis 1O6X  Ribosomal protein S6 S6 ( A. aeolicus ) Φ-Value analysis 2J5A  S6 ( T. thermophilus ) Φ-Value analysis 1RIS  RNA binding domain (RBD) U1A (Human) Φ-Value analysis 1FHT 
α + β (β-hairpin-α-hairpin repeat) Ankyrin repeat AnkyrinR D34 (Human) Minimal Φ-value analysis 1N11   Ankyrin repeats in tumor suppressor p16 (Human) Φ-Value analysis 1BI7  Cell-cycle inhibitor p19ink4D (Human) WT kinetics 1BD8  Myotrophin (Rat) Φ-Value analysis 2MYO  Neurogenic locus notch receptor domain (Drosophila) Minimal Φ-value analysis, WT redesign 1OT8 [125,126]
α + β (Cell-cycle regulatory proteins) Cell-cycle regulatory proteins CksHs1 (Human) Φ-Value analysis 1BUH   CksHs2 (Human) WT kinetics 1CKS  Suc1 ( S. pombe ) Φ-Value analysis 1PUC 
α + β (Lysozyme-like) Lysozyme-like Lysozyme (Hen Egg White) WT kinetics 1E8L   α-Lactalbumin (Bovine) WT kinetics 1F6S  α-Lactalbumin (Goat) Minimal Φ-value analysis, Hydrogen exchange 1HFY [131,132]  Milk lysozyme (Dog) Hydrogen exchange 1EL1 [131,133]
α + β (β-grasp: ubiquitin-like) Immunoglobulin-binding domains Protein G ( Streptococcus ) Φ-Value analysis 2IGD  [42,134,135] Immunoglobulin light chain-binding domain of Protein L ( P. magnus ) Φ-Value analysis 2PTL  Ubiquitin-like c-Raf1 RBD (Human) Φ-Value analysis 1RFA [134,135] Ubiquitin (Human) Minimal Φ-value analysis 1UBQ  Ubiquitin (Yeast) Φ-Value analysis 1Q0W 
All-β (Ig-like β-sandwich) Fibronectin type III CAfn2 ( B. circulans ) Φ-Value analysis 1K85  [15,19] FnIII-9 (Human) WT kinetics 1FNF  FnIII-10 (Human) Φ-Value analysis 1FNF  TNfn3 (Human) Φ-Value analysis 1TEN  Immunoglobulin TI I27 (Human) Φ-Value analysis 1TIT  CD2 (Rat) Minimal Φ-value analysis 1HNG  Various antibody domains (V L , C L , C H 2, C H 3) WT kinetics [139–142] 
All-β (Lipocalins) Lipocalins CRABP I (Mouse) WT kinetics 2CBR [143,144] [32,143] CRBP II (Rat) WT kinetics 1OPA  IFABP (Rat) Minimal Φ-value analysis 1IFC [31,32,143,145] ILBP (Rat) Minimal Φ-value analysis 1O1V b [31,32]
All-β (OB-fold) Nucleic acid-binding proteins Bc-Csp ( B. caldolyticus ) Φ-Value analysis 1C9O [146,147] [146,148] CspA ( E. coli ) Hydrogen exchange 1MJC  Bs-CspB ( B. subtilis ) Φ-Value analysis 1CSP  Tm-Csp ( T. maritima ) WT kinetics 1G6P 
All-β (PDZ domain-like) PDZ domain-like PDZ2 domain from PTP-BL (Mouse) Φ-Value analysis 1GM1   Third PDZ domain from synaptic protein PSD-95 (Rat) Hydrogen exchange Φ-value analysis 1BE9 [151,152]
All-β (SH3-like barrel) Chromo domain-like DNA-binding protein Sso7d ( S. solfataricus ) Φ-Value analysis 1SSO  [21,153] SH3-domain α-Spectrin SH3-domain (Chicken) Φ-Value analysis, WT redesign 1SHG [22,154] Fyn proto-oncogene tyrosine kinase SH3-domain (Chicken) Φ-Value analysis, NMR dispersion 1FYN b [23,24,155,156] Actin binding protein ABP1 (Yeast) NMR dispersion 1JO8  Phosphatidylinositol 3-kinase SH3-domain (Cow) WT kinetics 2PNI  c-src protein tyrosine kinase (Chicken) Φ-Value analysis 1SRM 
All-β (WW domain-like) WW domain Formin Binding Protein 28 (Mouse) Φ-Value analysis 1E0L [8,158] Mitotic rotamase PIN1 (Human) Φ-Value analysis 1PIN [48,159] Yap65 WW domain (Human) WT kinetics 1JMQ 
Coiled coil proteins (Parallel coiled-coil) Leucine zipper domain GCN4 (Yeast) WT kinetics, Minimal Φ-value analysis 2BNI [161,162] c-Jun (Human) Dimer thermodynamics 1JUN  c-Fos (Human) Dimer thermodynamics 1FOS  a Comparative references are those in which the folding mechanisms/pathways of homologous proteins are compared and discussed.
PubMed ID is not available.
Published in 2008
Materials and methods 1) Import native lysozyme sequence (gi:45384212) from NCBI and structure (PDB 1E8L ) from PDB websites 2) Run lysozyme in Ab initio mode to start folding independently from the o... iginal protein sequence.
Publication Year: 2008
Conformation-independent structural comparison of macromolecules with ProSMART.
(2014) Acta Crystallogr D Biol Crystallogr 70
PubMed: 25195761 | PubMedCentral: PMC4157452 | DOI: 10.1107/S1399004714016241
Multi-model comparative analysis of a solution NMR structure of hen egg-white lysozyme (PDB entry 1e8l ).
Publication Year: 2014
Published in 2015
In an interesting twist, the refined NMR structure of HEWL shows that the inward or buried conformation of Glu35 is popular in solution (PDB entry 1e8l ; Schwalbe et al. , 2001 ▶ ).
Publication Year: 2015
Structural images The structure of Lyz was represented with PyMOL (The PyMOL Molecular Graphics System, Version 220.127.116.11 Schrödinger, LLC) using the pdb-entry 1E8L of an NMR based solution stru... ture of hen egg white lysozyme [ 42 ] to visualize the most probable PEGylation sites as well as the protein residues relevant for evaluation of the experimental data.
g004 Fig 4 Ribbon structure of hen egg white lysozyme (pdb entry 1E8L).
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.