Citations in PubMed

Primary Citation PubMed: 16293754 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

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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Identification of hot-spot residues in protein-protein interactions by computational docking.

(2008) BMC Bioinformatics 9

PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447

Table 6 Additional dataset of complexes used in this work Complex a Res b Receptor Ligand Receptor PDB Res (Id) b Ligand PDB Res(Id) b Complex type c X-ray subunits 1CBW 2.60 Chymotrypsin BPTI 4CHA 1.... 8 4PTI 1.50 U/U 1PM9 1.70 IL-6R IL-6 1N26 2.40 1ALU 1.90 U/U N/A N/A KDR VEGF 2P2H 1.95 1VFP 2.50 U/U N/A N/A trkC Neurotrophin-3 1WWC 1.90 1NT3 2.40 U/U 2BTF 2.55 Rabbit actin Bovine profilin I 1J6Z 1.54 1PNE 2.00 U/U 1DVF 1.90 E5.2 D1.3 - - 1VFA 1.80 B/U N/A N/A sHIR Insulin 2DTG 3.80 2C8Q 1.95 U/U NMR subunits N/A N/A GPIIbIIIa Kistrin 1TYE 2.90 1N4Y NMR U/U N/A N/A bFGF FGFR1b 4FGF 1.60 1WVZ NMR U/U N/A N/A IGF-1R IGF-1 1IGR 2.60 2GF1 NMR U/U N/A N/A IGF-1bp IGF-1 1ZT3 1.80 2GF1 NMR U/U Homology-based modeled subunits N/A N/A E9 DNase Im2 1FSJ 1.80 1FR2 d (66%) U/M N/A N/A AChR Erabutoxin 2BG9 4.00 5EBX 2.00 cryo- EM/U N/A N/A AChR NmmI 2BG9 4.00 1V6P 0.87 cryo- EM/U 1Z92 2.80 IL-2 receptor IL-2 (human) 2B5I d (100%) 1M47 1.99 M/U N/A N/A IL-2 beta receptor(human) IL-2 (murine) 2B5I d (99%) 1M48 d (64%) M/M N/A N/A IL-2 alpha receptor(murine) IL-2 (murine) 1NWV d (22%) 1M48 d (64%) M/M N/A N/A IL-4/IL-4bp GammaC 1IAR 2.30 2B5I d (99%) U/M N/A N/A gp75 Neurotrophin-3 1LNL d (18%) 1NT3 2.40 M/U N/A N/A CD48 CD2 2DRU d (39%) 1CDC 2.00 M/U N/A N/A Calcineurin CaM 1AUI d (59%) 1LKJ NMR M/U 2D9Q 2.80 hG-CSFbp hG-CSF 2D9Q d (99%) 1RHG 2.20 M/U a PDB Code; N/A, Not Available; b Resolution in Å or (Id): sequence identity with template in case of model; c B, Bound; U, Unbound; M, Model; cryo-EM, cryoelectron microscopy structures classified as modeled structures because of the low resolution compared to crystallographic or NMR structures, d PDB code of the template structure used for modelling However, only a few of the 94 known hot-spots were detected, so the corresponding sensitivity ( S = 15%) was lower than that of the initial dataset ( S = 24%).

Publication Year: 2008


C17 prevents inflammatory arthritis and associated joint destruction in mice.

(2011) PLoS One 6

PubMed: 21799806 | PubMedCentral: PMC3143151 | DOI: 10.1371/journal.pone.0022256

Blue sequence denotes structure-confirmed alpha-helical secondary structure elements of respective cytokine (IL-2, PDB 2B5I; IL-4, PDB 1ITM; IL-13, PDB 1IKO; IL-15, PDB 2PSM; IL-21, PDB 2QQP).

Publication Year: 2011


Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure.

(2012) Bioinformatics 28

PubMed: 22210869 | PubMedCentral: PMC3307105 | DOI: 10.1093/bioinformatics/btr717

(b) The interleukin-2 cytokine receptor complex (PDB: 2B5I) shown with an 8μM inhibitor (PDB: 1M48).

Publication Year: 2012


Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

(2012) BMC Bioinformatics 13

PubMed: 22417279 | PubMedCentral: PMC3359218 | DOI: 10.1186/1471-2105-13-39

The residues most often involved in pocket formation (defined as those residues having the top 25% of Provar scores, ≥ 0.364 in this case) across 17 apo structures of functionally diverse IL-2... homologues are colored red on the molecular surface of IL-2 in a receptor bound conformation [PDB: 2B5I ].

In order to map Provar results for Figures 9 , 10A and 10B onto a receptor-bound structure, the receptor-bound IL-2 chain [PDB: 2B5I ] was included in the MUSTANG alignments, but ignored during Provar calculations.

Publication Year: 2012


Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.

(2012) Nat Immunol 13

PubMed: 23104097 | PubMedCentral: PMC3501574 | DOI: 10.1038/ni.2449

Structure Determination and Refinement The IL-15 quaternary complex structure was solved by molecular replacement using individual IL-2Rβ and γ c subunits from PDB 2B5I and the IL-15&#... 02014;IL-15Rα complex from PDB 2Z3Q.

The IL-15 quaternary complex, containing its private alpha-receptor and the shared signaling receptors IL-2Rβ and γ c , assembles in a nearly identical fashion as the IL-2 quaternary complex ( Fig. 1b left, PDB code 2B5I), with IL-2Rβ binding to “site I” and γ c to “site II” on the cytokine.

Publication Year: 2012