Primary Citation PubMed: 16293754
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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.
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.
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