Citations in PubMed

Primary Citation PubMed: 1881880 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 13

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.

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Variation in structural location and amino acid conservation of functional sites in protein domain families.

(2005) BMC Bioinformatics 6

PubMed: 16122386 | PubMedCentral: PMC1215474 | DOI: 10.1186/1471-2105-6-210

PDB identifiers from top to bottom: 1PC8 (B: 5–131), 1TFM (B: 5–131), 2MLL (B: 5–131), 1CE7 (B: 5–131), 1ONK (B: 9–135), 1PUM (B: 9–135), 1M2T (B: 257&#... 02013;383), 1OQL (B:13–139), 1ABR (B: 13–139), 2AAI (B: 8–134), 1HWO (B: 10–135), 1HWP (B: 10–135), 1HWN (B:10–135), 1HWM (B:3–266), 1V6U (A: 312–436), 1ISW (A:312–436), 1ISV (A:312–436), 1ITO (A:312–436), 1V6W (A: 312–436), 1V6X (A: 312–436), 1XYF (A:312–436), 1ISY (A: 312–436), 1ISZ (A:312–436), 1V6V (A:312–436), 1ISX (A:312–436), 1KNM (A:7–131), 1KNL (A:9–133), 1BFM 1MC9(A:9–133), 1QXM (A: 29–157), 1PUM (B: 140–262), 1M2T (B: 390–510), 1ONK (B: 140–262), 1OQL (B: 140–262), 1PC8 (B: 136–254), 1TFM (B: 136–254), 2MLL (B: 136–254), 1CE7 (B:136–254), 2AAI (B: 138–261), 1ABR (B: 143–266), 1HWO (B: 138–262), 1HWP (B: 138–262), 1HWM (B: 138–262), 1HWN (B: 139–263), 1FWU (A: 3–123), 1DQG (A: 4–124), 1DQO (A: 4–124), 1FWV (A: 3–123) Alternating locations of functional sites are especially prominent in DNA binding domains, like the C2H2-zinc finder and homeodomains [ 22 ].

Publication Year: 2005


Relating destabilizing regions to known functional sites in proteins.

(2007) BMC Bioinformatics 8

PubMed: 17470296 | PubMedCentral: PMC1890302 | DOI: 10.1186/1471-2105-8-141

Pdb id a Holo-pdb ids b N res c F res d ASA e F ASA f Cleft g Small 1e1a 13 4.2 272 2.1 T 1e3f 1bm7 , 1e4h , 1e5a , 1eta , 1tha 8 6.9 193 1.0 T 1gu7 1guf , 1n9g 31 8.5 1158 3.7 T 1gud 1rpj 24 8.3 976 ... .4 T 1gus 1gug , 1gun , 1guo 4 6.0 119 0.9 F 1gus h 1gug , 1gun , 1guo 14 20.9 110 0.8 F 1gxy 1og1 , 1og3 , 1og4 24 10.8 947 8.7 T 1hf8 1hfa , 1hg2 , 1hg5 4 1.5 329 1.4 F 1hhq 1hiy , 1b4s , 1b99 , 1bux 17 11.3 1006 2.8 T 1is5 1is3 , 1is4 , 1is6 22 16.4 663 3.0 T 1jcf 1jcg 34 10.1 820 5.6 F 1odl 1odi , 1odj 25 10.7 339 0.8 T 1ofn 1oi6 15 7.4 669 4.0 T 1tm2 1tjy 19 6.1 437 3.2 T 1upq 1upr 12 11.2 783 11.9 T 1usg 1usk , 1usi 15 4.3 268 1.0 T 1usl 2bes , 2bet 18 11.5 505 3.9 T 1w1h 1w1d , 1w1g 10 6.6 560 6.2 T 1w2i 1w2i 8 8.9 450 5.0 F 1w37 1w3i , 1w3n , 1w3t 12 4.1 107 0.3 T 1y2t 1y2x , 1y2w 27 19.0 1191 5.6 F Polysaccharide 1nof 12 3.1 471 3.2 T 1o88 15 4.2 472 3.5 T 1ob0 1e3z 41 8.5 1572 8.9 T 1ogb 1e6n , 1e6r , 1h0g , 1h0i , 1ogg 16 3.2 565 1.5 T 1qhz 1qi2 , 8a3h , 4a3h , 1e5j , 1qi0 14 4.6 590 5.2 T 1qjv 10 2.9 265 1.8 T 1uuq 1uz4 16 3.9 256 1.7 T 1w0n 1ux7 8 6.7 642 11.2 T 1w6z 1sf7 , 1sfb , 1sfg 20 15.5 891 13.6 T 1w9s 1w9t , 1w9w 12 9.0 376 5.9 F Peptide 1c7k 9 6.8 275 4.2 T 1e5t 1e8m , 1e8n , 1o6g , 1qfs , 1uop 18 2.5 485 1.7 T 1ea7 7 2.3 97 0.9 T 1gt9 1gtj , 1gtl 21 5.9 450 3.4 F 1kl4 1hqq , 1kl3 , 1kl5 , 1rsu 17 14.2 854 4.2 T 1oes 1g1f , 1g1g , 1g1h , 1ptt , 1ptu 16 5.7 885 6.6 T 1r29 1r2b 29 23.8 1760 13.8 F Protein 1e3f 1qab , 1rlb 15 13.0 971 5.0 F 1e6l 1bdj 10 7.9 775 11.7 F 1e6l 1a0o , 1eay , 1ffg , 1ffs , 1ffw 15 11.8 1212 18.4 T 1eao 1e50 , 1h9d 26 22.8 1819 28.2 F 1f2x 12 9.5 604 5.2 F 1gcp 1gcq 21 31.3 1405 33.2 F 1gqv 2bex 36 26.7 2246 28.9 F 1obq 1gka 22 12.2 1023 6.1 T 1sif 1cmx , 1fxt , 1nbf , 1otr , 1q5w , 1s1q , 1uzx 14 19.7 937 21.7 T 1tgr 1h59 15 28.8 1236 29.5 T 1uns 1jck 19 8.1 1620 13.5 F 1uns 1jwm 20 8.5 1386 11.6 F 1uol 1gzh , 1kzy 18 9.2 1301 13.1 F 1uq4 2aai 42 16.0 2796 21.6 F 1w53 12 14.3 770 8.8 T Nucleic acid 1e7l 8 5.1 352 2.0 T 1eao 1h9d , 1hjb 18 15.8 1375 21.3 F 1gqv 1hi3 , 1hi4 , 1hi5 9 6.7 245 3.2 T 1gv2 1h88 , 1h89 , 1mse 30 29.1 2289 30.2 T 1o7i 5 4.3 497 7.4 F 1okb 1emh , 1emj , 1q3f , 1ssp , 2ssp , 4skn 30 13.5 1539 15.0 T 1uol 1tsr , 1tup 19 9.7 1229 12.4 F 1uq4 1apg , 1br5 17 6.5 364 2.8 T 1utx 10 15.2 691 9.0 F 1vyi 10 9.0 1009 15.0 F Lipid 1obq 1h91 , 1i4u , 1s2p , 1s44 21 11.6 350 2.1 T 1qmd 14 3.8 465 2.9 F Metal 1e6l 1chn , 1ymv 7 5.5 350 5.3 T 1qmd 1kho 6 1.6 67 0.4 T Peptide-Protein 1mix 1mk7 , 1mk9 26 12.6 1526 11.9 F Small-Metal 1h1y 19 8.6 365 2.2 T 1h6l 2poo , 1h6l 16 4.5 627 4.4 T 1oid 1ho5 , 1hp1 , 1hpu 19 3.6 872 3.9 F Polysaccharide-Metal 1gkb 1bxh , 1cjp , 1c57 , 1ces , 1dq1 , 1gkb , 3cna , 3enr 19 8.0 586 1.8 F Lipid-Metal 1umv 1pob , 1umv , 1c1j 17 13.9 492 3.8 T Protein-Metal 1o6v 1o6s 49 10.6 2224 11.3 F Properties of known binding sites of the dataset proteins.

Publication Year: 2007


Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand.

(2000) J Exp Med 191

PubMed: 10748229 | PubMedCentral: PMC2193177 | DOI: null

(A) Ribbon diagrams comparing the crystal structures of Cys-MR, a portion of the ricin B chain (residues 1–136 with N-linked carbohydrates omitted; PDB code 2AAI [reference 36 ]), and ... uman aFGF (PDB code 2AXM [reference 45 ]).

(D) Comparison of the stacking interactions between tryptophan and galactose rings from the complexed structures of Cys-MR (yellow bonds), the galactose binding mutant of mannose-binding protein (reference 52 ; PDB code 1AFB, green bonds), and ricin B chain (reference 36 ; PDB code 2AAI, purple bonds).

Publication Year: 2000


Small-molecule inhibitor leads of ribosome-inactivating proteins developed using the doorstop approach.

(2011) PLoS One 6

PubMed: 21455295 | PubMedCentral: PMC3063779 | DOI: 10.1371/journal.pone.0017883

Conformation 1 represents the Tyr80 conformation in apo -RTA crystal structures (Protein Data Bank [PDB] IDs: 1IFT [32] , 1RTC [33] , 1IL5 [24&#... 0005d; , and 2AAI [34] ).

Publication Year: 2011


Toxin-based therapeutic approaches.

(2010) Toxins (Basel) 2

PubMed: 22069564 | PubMedCentral: PMC3153180 | DOI: 10.3390/toxins2112519

Ricin toxin is translated as a single glycosylated polypeptide that is composed of a catalytic A domain and a lectin B domain (see 3D structure (PDB Entry: 2aai) in the left panel; the colors of the s... bunits correspond to those in the scheme).

Publication Year: 2010


Structure of RiVax: a recombinant ricin vaccine.

(2011) Acta Crystallogr D Biol Crystallogr 67

PubMed: 21904036 | PubMedCentral: PMC3169317 | DOI: 10.1107/S0907444911026771

RTB is known to contain a binding domain that binds to cell surface glycoproteins or glycolipids containing galactose, thereby facilitating toxin uptake (Fig. 1 ▶ b , based on PDB entry 2aai ;... Rutenber et al. , 1991 ▶ ; Ganguly & Mukhopadhyay, 2006 ▶ ).

An examination of the 2aai crystal structure shows that the RTA epitope recognized by UNIVAX 70/138 is distant from RTB and its carbohydrate-binding sites, suggesting that this MAb does not neutralize ricin toxin by a direct steric effect on the lectin function of the toxin.

( b ) Structure of the ricin AB toxin determined by Rutenber et al. (1991 ▶ ) (PDB entry 2aai ).

Publication Year: 2011


Sub-domains of ricin's B subunit as targets of toxin neutralizing and non-neutralizing monoclonal antibodies.

(2012) PLoS One 7

PubMed: 22984492 | PubMedCentral: PMC3439471 | DOI: 10.1371/journal.pone.0044317

(Upper panel) Surface depiction of ricin holotoxin produced by PyMOL and based on PDB file 2AAI [46] .

Alignment of the B chain sequences from ricin (PDB 2AAI) and RCA-I (PDB 1RZO) using BLAST ( www.ncbi.nlm.nih.gov ).

Publication Year: 2012


Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody.

(2012) PLoS One 7

PubMed: 23285112 | PubMedCentral: PMC3526572 | DOI: 10.1371/journal.pone.0052613

The crystal structure of ricin has been solved by X-ray crystallography at 2.5 Å [7] (PDB ID: 2AAI).

Publication Year: 2012


Analysis of castor bean ribosome-inactivating proteins and their gene expression during seed development.

(2013) Genet Mol Biol 36

PubMed: 23569411 | PubMedCentral: PMC3615529 | DOI: 10.1590/S1415-47572013005000005

The crystallographic model of ricin (pdb code 2AAI) was used with the software Swiss-Pdb-Viewer (version 4.0.1) ( Guex and Peitsch, 1997 ) to illustrate the active site of the RIPs and their associati... n with lipase activity.

Publication Year: 2013


Disruption of the putative vascular leak peptide sequence in the stabilized ricin vaccine candidate RTA1-33/44-198.

(2013) Toxins (Basel) 5

PubMed: 23364220 | PubMedCentral: PMC3640533 | DOI: 10.3390/toxins5020224

RTA1-33/44-198 R48C/T77C (PDB 3LC9) could be aligned with the RTA (PDB 2AAI) with an rmsd of 0.69 over 156 C α .

Publication Year: 2013


Toxin instability and its role in toxin translocation from the endoplasmic reticulum to the cytosol.

(2013) Biomolecules 3

PubMed: 24970201 | PubMedCentral: PMC4030972 | DOI: 10.3390/biom3040997

The CtxB pentamer recognizes GM1 gangliosides on the host cell surface, while CtxA1 is an ADP-ribosyltransferase that elevates intracellular cAMP levels by activating the stimulatory α subunit... of the heterotrimeric G protein; ( b ) Ribbon diagram of ricin toxin (Rtx; PDB 2AAI, [ 34 ]).

Publication Year: 2013


Differential neutralizing activities of a single domain camelid antibody (VHH) specific for ricin toxin's binding subunit (RTB).

(2014) PLoS One 9

PubMed: 24918772 | PubMedCentral: PMC4053406 | DOI: 10.1371/journal.pone.0099788

X-ray crystal structure of ricin holotoxin visualized using PyMOL and based on PDB file 2AAI [55] .

Publication Year: 2014


Ricin trafficking in cells.

(2015) Toxins (Basel) 7

PubMed: 25584427 | PubMedCentral: PMC4303813 | DOI: 10.3390/toxins7010049

The crystal structure (PDB code 2AAI [ 11 ]) was viewed in Chimera (UCSF) and is shown from the side with the receptor-binding surfaces of ricin toxin B chain (RTB, green) facing downwards.

Publication Year: 2015