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PDB ID Mentions in PubMed Central Article count: 1

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PDB ID Mentions in PubMed Central

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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