Citations in PubMed

Primary Citation PubMed: 9087403 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

(2005) BMC Struct Biol 5

PubMed: 16105176 | PubMedCentral: PMC1201154 | DOI: 10.1186/1472-6807-5-15

Table 1 The dataset of obligatory and non-obligatory polypeptide chains identified from the PDB LIST OF NON-OBLIGATORY PROTEIN-CHAINS PDB Representative-chain Partner-chain Resolution Names of protein... 1dx5 I M 2.30 Thrombomodulin, Thrombin Heavy Chain 1gua A B 2.00 Rap1A, C-Raf1 1efu A B 2.50 Elongation Factor Tu, Elongation Factor Ts 1avw B A 1.75 Trypsin, Trypsin Inhibitor 1emv A B 1.70 Immunity Protein Im9, Colicin E9 1ay7 B A 1.70 Barstar, Guanyl-Specific Ribonuclease Sa 1stf E I 2.37 Papain (Cys 25 Carboxymethylated), Papain (Cys 25 Carboxymethylated) 3eza B A NMR Histidine-Containing Phosphocarrier Protein H, Phosphotransferase System, Enzyme I 1ggr B A NMR Phosphocarrier Protein Hpr, Pts System, Glucose-Specific Iia Component 1pyt B A 2.35 Procarboxypeptidase A, Procarboxypeptidase A 1pyt B D 2.35 Procarboxypeptidase A, Chymotrypsinogen C 1fle I E 1.90 Elafin, Elastase 1sgp I E 1.40 Turkey Ovomucoid Inhibitor, Streptomyces Griseus Proteinase B 1ycs A B 2.20 P53, P53 1ycs B A 2.20 P53, P53 1efn A B 2.50 Fyn Tyrosine Kinase, Hiv-1 Nef Protein 1efn B A 2.50 HIV-1 Nef Protein, Fyn Tyrosine Kinase 1tx4 A B 1.65 P50-Rho GAP, Transforming protein rhoa 1tx4 B A 1.65 Transforming protein Rhoa, P50-Rho GAP 1a2k C A 2.50 Nuclear Transport Factor 2, Nuclear Transport Factor 2 1fin A B 2.30 Cyclin-Dependent Kinase 2, Cyclin A 1fin B A 2.30 Cyclin A, Cyclin-Dependent Kinase 2 1ak4 A C 2.36 Cyclophilin A, Hiv-1Capsid 1ak4 C A 2.36 Hiv-1Capsid, Cyclophilin A 1dhk A B 1.85 Porcine Pancreatic Alpha-Amylase, Bean Lectin-Like Inhibitor 1gla F G 2.60 Glycerol Kinase, Factor III Glc 1ydr E I 2.20 C-Amp-Dependent Protein Kinase, Protein Kinase Inhibitor Peptide 2pcc A B 2.30 Cytochrome C Peroxidase, Cytochrome C 2pcc B A 2.30 Cytochrome C, Cytochrome C Peroxidase 1d2z A B 2.00 Death Domain Of Pelle, Death Domain Of Tube LIST OF OBLIGATORY PROTEIN-CHAINS PDB Representative chain Partner chain Resolution Names of proteins 1bmq B A 2.50 Interleukin-1 Beta Convertase, Interleukin-1 Beta Convertase 1qdl B A 2.50 Anthranilate Synthase (Trpg-Subunit), Anthranilate Synthase (Trpe-Subunit) 1poi B A 2.50 Glutaconate Coenzyme A-Transferase, Glutaconate Coenzyme A-Transferase 1ihf B A 2.50 Integration Host Factor, Integration Host Factor 1poi B C 2.50 Glutaconate Coenzyme A-Transferase, Glutaconate Coenzyme A-Transferase 1bcr B A 2.50 Serine Carboxypeptidase II, Serine Carboxypeptidase II 1wdc A B 2.00 Scallop Myosin, Scallop Myosin 1wdc A C 2.00 Scallop Myosin, Scallop Myosin 1ryp 1 I 1.90 20S Proteasome, 20S Proteasome 1ryp 1 J 1.90 20S Proteasome, 20S Proteasome 1ryp 1 S 1.90 20S Proteasome, 20S Proteasome 1ryp 1 T 1.90 20S Proteasome, 20S Proteasome 1ryp 1 Z 1.90 20S Proteasome, 20S Proteasome 1ryp 1 2 1.90 20S Proteasome, 20S Proteasome 1kve A B 1.80 Smk Toxin, Smk Toxin 1luc A B 1.50 Bacterial Luciferase, Bacterial Luciferase 1fm0 E D 1.45 Molybdopterin Convertin Factor, Subunit 2, Molybdopterin Convertin Factor, Subunit 1 1fm0 D E 1.45 Molybdopterin Convertin Factor, Subunit 1, Molybdopterin Convertin Factor, Subunit 2 1h2r S L 1.40 Periplasmic [Nife] Hydrogenase Small Subunit, [Nife] Hydrogenase Large Subunit 1h2r L S 1.40 Periplasmic [Nife] Hydrogenase Large Subunit, Periplasmic [Nife] Hydrogenase Small Subunit 1svf C D 1.40 Fusion Glycoprotein, Fusion Glycoprotein 1svf B A 1.40 Fusion Glycoprotein, Fusion Glycoprotein 1hbn B C 1.16 Methyl-Coenzyme M Reductase I Beta Subunit, Methyl-Coenzyme M Reductase I Gamma Subunit 1ycp K J 2.50 Epsilon Thrombin, Epsilon Thrombin 1hfe S L 1.60 Fe-Only Hydrogenase (Smaller Subunit), Fe-Only Hydrogenase (Larger Subunit) 1f95 A B NMR Dynein, Dynein 1a2k A B 2.50 Nuclear Transport Factor 2, Nuclear Transport Factor 2 2thi A B 2.50 Thiaminase I, Thiaminase I 1e5d A B 2.50 Rubredoxin: Oxygen Oxidoreductase, Rubredoxin: Oxygen Oxidoreductase 1b55 B A 2.40 Tyrosine-Protein Kinase Btk, Tyrosine-Protein Kinase Btk 3nos A B 2.40 Endothelial Nitric-Oxide Synthase, Endothelial Nitric-Oxide Synthase 1qfx A B 2.40 pH 2.5 Acid Phosphatase, pH 2.5 Acid Phosphatase 2tmk A B 2.40 Thymidylate Kinase, Thymidylate Kinase 1f37 A B 2.30 Ferredoxin [2Fe-2S], Ferredoxin [2Fe-2S] 1qdn A B 2.30 N-Ethylmaleimide Sensitive Fusion Protein (N), N- Ethylmaleimide Sensitive Fusion Protein (N) 1dcp A B 2.30 Dcoh, Dcoh 1dcp A C 2.30 Dcoh, Dcoh 1dcp A D 2.30 Dcoh, Dcoh 1dcp A E 2.30 Dcoh, Dcoh 1del B A 2.20 Deoxynucleoside Monophosphate Kinase, Deoxynucleoside Monophosphate Kinase 1otg A B 2.10 5-Carboxymethyl-2-Hydroxymuconate Isomerase, 5-Carboxymethyl-2-Hydroxymuconate Isomerase 1bft A B 2.00 Nuclear Factor Nf-Kappa-B P65, Nuclear Factor Nf-Kappa-B P65 1coz A B 2.00 Glycerol-3-Phosphate Cytidylyltransferase, Glycerol-3-Phosphate Cytidylyltransferase 1mka A B 2.00 Beta-Hydroxydecanoyl Thiol Ester Dehydrase, Beta-Hydroxydecanoyl Thiol Ester Dehydrase 1b66 A B 1.90 6-Pyruvoyl Tetrahydropterin Synthase, 6-Pyruvoyl Tetrahydropterin Synthase 1otf A C 1.90 4-Oxalocrotonate Tautomerase, 4-Oxalocrotonate Tautomerase 1otf A D 1.90 4-Oxalocrotonate Tautomerase, 4-Oxalocrotonate Tautomerase 1otf A E 1.90 4-Oxalocrotonate Tautomerase, 4-Oxalocrotonate Tautomerase 1j9l A B 1.90 Stationary Phase Survival Protein, Stationary Phase Survival Protein 1dfn A B 1.90 Defensin HNP-3 – Chain A, Defensin HNP-3 – Chain B 1b93 A B 1.90 Methylglyoxal Synthase, Methylglyoxal Synthase 1b93 A C 1.90 Methylglyoxal Synthase, Methylglyoxal Synthase 1ext B A 1.85 Tumor Necrosis Factor Receptor, Tumor Necrosis Factor Receptor 1kve A C 1.80 Smk Toxin, Smk Toxin 1atl A B 1.80 Atrolysin C, Atrolysin C 1d2v A B 1.75 Myeloperoxidase, Myeloperoxidase 1tvx B A 1.75 Neutrophil Activating Peptide 2 Variant, Neutrophil Activating Peptide 2 Variant 1tvx B C 1.75 Neutrophil Activating Peptide 2 Variant, Neutrophil Activating Peptide 2 Variant 6gsv A B 1.75 Mu Class Glutathione S-Transferase Of Isoenz, Mu Class Glutathione S-Transferase Of Isoenz 1qsg G E 1.75 Enoyl-Reductase, Enoyl-Reductase 1qsg G F 1.75 Enoyl-Reductase, Enoyl-Reductase 1qsg G H 1.75 Enoyl-Reductase, Enoyl-Reductase 1a2z A B 1.73 Pyrrolidone Carboxyl Peptidase, Pyrrolidone Carboxyl Peptidase 1a2z A D 1.73 Pyrrolidone Carboxyl Peptidase, Pyrrolidone Carboxyl Peptidase 1mjh A B 1.70 ATP-Binding Domain Of Protein Mj0577, ATP-Binding Domain Of Protein Mj0577 1dqi A B 1.70 Superoxide Reductase, Superoxide Reductase 1dqi A D 1.70 Superoxide Reductase, Superoxide Reductase 1jqc B A 1.61 Protein R2 Of Ribonucleotide Reductase, Protein R2 Of Ribonucleotide Reductase 1f74 A C 1.60 N-Acetyl-Neuraminate Lyase, N-Acetyl-Neuraminate Lyase 3pvi A B 1.59 Pvuii Endonuclease, Pvuii Endonuclease 1f9z A B 1.50 Glyoxalase I, Glyoxalase I 1jr8 A B 1.50 Erv2 Protein, Mitochondrial, Erv2 Protein, Mitochondrial 1a4i B A 1.50 Methylenetetrahydrofolate Dehydrogenase / Me, Methylenetetrahydrofolate Dehydrogenase / Me 1dvj A B 1.50 Orotidine 5'-Phosphate Decarboxylase, Orotidine 5'-Phosphate Decarboxylase 1qh4 A B 1.41 Creatine Kinase, B Chain, Creatine Kinase, B Chain 2tnf A B 1.40 Tumor Necrosis Factor Alpha, Tumor Necrosis Factor Alpha 3sdh A B 1.40 Hemoglobin I (Homodimer) (Carbon-Monoxy) – C, Hemoglobin I (Homodimer) (Carbon-Monoxy) – C 1i0h A B 1.35 Manganese Superoxide Dismutase Y174F Mutant, Manganese Superoxide Dismutase Y174F Mutant 1dbf A B 1.30 Chorismate Mutase, Chorismate Mutase 1qks A B 1.28 Cytochrome Cd1 Nitrite Reductase, Cytochrome Cd1 Nitrite Reductase 1hbn B E 1.16 Methyl-Coenzyme M Reductase I Beta Subunit, Methyl-Coenzyme M Reductase I Beta Subunit

Publication Year: 2005


Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography.

(2009) BMC Struct Biol 9

PubMed: 19706171 | PubMedCentral: PMC2739207 | DOI: 10.1186/1472-6807-9-56

protein Abbreviation PDB-ID* Z-score rmsd [Å] L ali N res % ID cephalosporin acylase CA 1oqz 17.0 3.6 360 684 11 penicillin V acylase PVA 3pva 16.2 3.0 222 334 6 conjugated bile acid (= choloy... glycine) hydrolase CBAH 2bjf 16.2 3.1 224 328 6 penicillin G acylase PGA 1k5s 15.4 3.4 244 557 11 IMP cyclohydrolase IMPC 2ntm 8.4 3.2 165 202 14 20 S proteasome - 1ryp 8.3 3.1 161 205 7 Only hits with a Z-score ≥ 7 and with an assigned cellular function are listed here.

Publication Year: 2009


Probing the anticancer mechanism of prospective herbal drug Withaferin A on mammals: a case study on human and bovine proteasomes.

(2010) BMC Genomics 11 Suppl 4

PubMed: 21143798 | PubMedCentral: PMC3005937 | DOI: 10.1186/1471-2164-11-S4-S15

We built three dimensional structure of h20S using multiple template comparative homology modelling based on the following X-ray crystal structures obtained from PDB (Protein Data Bank)[ 33 ]: b20S (b... vine 20S proteasome) at 2.75 Å resolution (PDB:1IRU), yeast 20S proteasome at 2.4 Å resolution (PDB:1RYP) and 20S proteasome from Archaeoglobus fulgidus (PDB:1J2Q).

Publication Year: 2010


JAMM: a metalloprotease-like zinc site in the proteasome and signalosome.

(2004) PLoS Biol 2

PubMed: 14737182 | PubMedCentral: PMC300881 | DOI: 10.1371/journal.pbio.0020002

Supporting Information Accession Numbers The accession numbers for the proteins discussed in this paper are 20S proteasomes (PDB ID 1RYP), AfJAMM (Entrez Protein ID NP_071023; PDB ID 1R5X), AM... H (Entrez Protein ID NP_006454), AtCSN5/AJH1 (Entrez Protein ID NP_173705), AtRpn11 (Entrez Protein ID NP_197745), C6.1A (Entrez Protein ID NP_077308), CeCSN5 (Entrez Protein ID NP_500841), CeRpn11 (Entrez Protein ID NP_494712), Csn5 (Entrez Protein ID NP_593131), Cul1 (Entrez Protein ID NP_594259), cytidine deaminase (PDB ID 1JTK), DmCsn5/CH5 (Entrez Protein ID NP_477442), DmRpn11/p37b (Entrez Protein ID AAF08394), EcRadC (Entrez Protein ID NP_418095), HsAMSH (Entrez Protein ID NP_006454), HsC6.1A (Entrez Protein ID NP_077308), HsCsn5 (Entrez Protein ID NP_006828), HsRpn11/POH1 (Entrez Protein ID NP_005796), JAB1 (Entrez Protein ID AAC17179), lambdaK (Entrez Protein ID AAA96551), Mov34 (Entrez Protein ID NP_034947), Mpr1p (Entrez Protein ID AAN77865), Nedd8 (Swiss-Prot ID Q15843), neurolysin (PDB ID 1I1I), Pad1p (Entrez Protein ID NP_594014), phage λ tail assembly protein K (Entrez Protein ID AAA96551), RadC (Entrez Protein ID NP_418095), Rpn11 (Entrez Protein ID AAN77865), SCF (PDB ID 1LDK), ScNP (PDB ID 1C7K), ScRpn11 (Entrez Protein ID AAN77865), Sic1 (Entrez Protein ID 1360441), SpCsn5 (Entrez Protein ID NP_593131), SpRpn11/Pad1 (Entrez Protein ID NP_594014), thermolysin (PDB ID 1FJQ), ubiquitin (Swiss-Prot ID P04838), UBP (PDB ID 1NB8), and UCH (PDB ID 1UCH).

Publication Year: 2004


BISC: binary subcomplexes in proteins database.

(2011) Nucleic Acids Res 39

PubMed: 21081561 | PubMedCentral: PMC3013763 | DOI: 10.1093/nar/gkq859

[The first eukaryotic proteasome structure was deposited in the PDB in April 1998 (PDB:1RYP).]

Publication Year: 2011


Novel interactions between actin and the proteasome revealed by complex haploinsufficiency.

(2011) PLoS Genet 7

PubMed: 21966278 | PubMedCentral: PMC3178594 | DOI: 10.1371/journal.pgen.1002288

(B) and (C) Surface rendering of the 20S core proteasome X-ray structure (1RYP.

Publication Year: 2011


Molecular mechanisms of bortezomib resistant adenocarcinoma cells.

(2011) PLoS One 6

PubMed: 22216088 | PubMedCentral: PMC3245226 | DOI: 10.1371/journal.pone.0027996

The Cys63Phe mutation was modeled into the crystal structure of the α5/β5/β6 yeast proteasome subunits bound to epoxomicin (PDB# 1G65) or bortezomib (PDB# 2F16) and into the ap... -form structure (PDB# 1RYP).

Publication Year: 2011


Homopiperazine derivatives as a novel class of proteasome inhibitors with a unique mode of proteasome binding.

(2013) PLoS One 8

PubMed: 23593271 | PubMedCentral: PMC3623906 | DOI: 10.1371/journal.pone.0060649

The structures were solved by molecular replacement using MOLREP [32] with the previously reported structure of 20 S proteasome (Protein Data Bank code 1RYP) as a starting model.

Publication Year: 2013


Interface-resolved network of protein-protein interactions.

(2013) PLoS Comput Biol 9

PubMed: 23696724 | PubMedCentral: PMC3656101 | DOI: 10.1371/journal.pcbi.1003065

0 residues overlapping 1 residue overlapping >1 residue overlapping Proteasome subunits (1RYP.

Publication Year: 2013


Analysis of bortezomib inhibitor docked within the catalytic subunits of the Plasmodium falciparum 20S proteasome.

(2013) Springerplus 2

PubMed: 24255860 | PubMedCentral: PMC3825223 | DOI: 10.1186/2193-1801-2-566

Construction & validation of the Pf 20S proteasome and docking of bortezomib within the catalytic subunits The crystal structures of the yeast 20S proteasome (PDB code:1RYP) (Groll et al.

Figure 1 Schematic representation showing structural overlay of the crystal structure of yeast 20S proteasome [PDB code:1RYP] (orange) and the Pf 20S proteasome model (yellow); (A) side-view and (B) top-view.

Comparison of the catalytic sites, substrate binding pockets and bortezomib binding in 3-D models of Pf 20S proteasome and crystal structure complex of yeast 20S proteasome The residues important for the catalytic activity, substrate binding pockets and maintenance of stability of the conformation of Thr1 via hydrogen bond essential for the Ntn hydrolases was obtained from the crystal structure of the yeast 20S proteasome (PDB code: 1RYP).

Publication Year: 2013