Table 2. DIRP specific positions mapping to binding sites in the human Ras complexes.
| Functional Group | Complexes | Description | Positions | Num | Ratio |
|---|---|---|---|---|---|
| RasGef | 1LFD | Interaction of Ras with RalGDS | G12, Y32, D33, P34, I36, E37, D38, S39, Y40, Q61, E62, E63, Y64, S65, A66, M67 | 7/16 | 43.7% |
| 1NVU 1NVX 1NVW 1NVV |
Feedback activation by Ras. GTP of the Ras-specific nucleotide exchange factor SOS | S17, T20, I21, Q22, I24, N26, H27, D30, E31, Y32, D33, P34, I36, E37, D38, Y40, K42, Q43, V44, D54, I55, D57, A59, G60, Q61, E63, Y64, S65, A66, M67, D69, Q70, Y71, R73, R102, R149 | 12/36 | 33.3% | |
| 1XD2 | Autoinhibition in the Ras activator Son of sevenless: ternary Ras:SOS:Ras*GDP complex | Q22, I24, N26, H27, D33, P34, I36, E37, D38, K42, Q43, V44, L56, E63, Y64, A66, M67, Q70, Y71, R149 | 7/20 | 35.0% | |
| 1BKD | The structural basis of the activation of Ras by Sos: H-Ras with SOS-1 | S17, I21, Y32, P34, Y40, D54, I55, D57, A59, G60, Q61, E63, Y64, S65, A66, M67, D69, Q70, Y71, R73, R102 | 8/21 | 38.1% | |
| RapGef | 3CF6 | Epac2 in complex with a cyclic AMP analogue and RAP1B | S17, T20, I21, H27, Y32, P34, E37, Y40, D54, I55, L56, D57, A59, G60, Q61, Y64, A66, M67, D69, Q70, Y71, Q99 | 9/22 | 40.9% |
| RasGap | 1WQ1 | The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants | A11, G12, G13, I21, Y32, D33, P34, I36, E37, D38, S39, Y40, G60, Q61, E62, E63, Y64, K88, D92 | 7/19 | 36.8% |
| Antobodies (Cancer supressors) | 2UZI | Tumour prevention by a single antibody domain targeting the interaction of signal transduction proteins with RAS | I21, V29, D33, P34, I36, E37, D38, Y40, Q61, Y64 | 4/10 | 40.0% |
| 2VH5 | HRAS(G12V) - ANTI-RAS FV (DISULFIDE FREE MUTANT) COMPLEX | I21, V29, D33, P34, I36, E37, D38, Y40, D57, Q 61, Y64 | 4/11 | 36.4% | |
| 3DDC | Ras effector interaction between tumour suppressor NORE1A and Ras switch II | I24, Q25, I36, D38, Y40, Y64, M67 | 2/7 | 28.6% | |
| Ras Binding Domain & PI3K | 1HE8 | Ras binding to its effector phosphoinositide 3-kinase gamma | I21, D33, I36, E37, D38, S39, Y40 | 2/7 | 28.6% |
| 3KUC 1GUA |
Complex of Rap1A(E30D/K31E) GDP with RafRBD(A85K/N71R) Ras/Rap effector specificity determined by charge reversal | I21, D33, I36, E37, D38, S39, Y40, R41 | 2/8 | 25.0% | |
| 3KUD | What makes Ras an efficient molecular switch: Ras-GDP interactions with mutants of Raf | I21, E37, D38, S39, Y40, R41 | 0/6 | 0.0% | |
| 1K8R | Ras-Byr2RBD complex: structural basis for Ras effector recognition | I36, E37, D38, S39, Y40, R41, D54 | 2/7 | 28.6% | |
| 1C1Y | c-Raf1 in complex with Rap1A and a GTP analogue | I21, I36, E37, D38, S39, Y40, R41 | 1/7 | 14.3% | |
| Other cases | 1ZC3 1ZC4 |
Ral-binding domain of Exo84 in complex with the active RalA | D47, G48, E49, T50, C51, L52, M67, G75, F78, V81, F82 | 1/11 | 9.1% |
| 2A9K 2A78 |
C3bot-NAD-RalA complex: Ral-A and Mono-ADP-ribosyltransferase C3 C3bot-RalA complex | T20, I21, Q22, L23, D69, Y71, M72, G75, L79, A83, V103, S106, D107, P110 | 4/14 | 28.6% | |
| 2C5L | PLC epsilon Ras association domain with HRas | I24, Q25, I36, D38, S39, Y40, D47, S127, Q131, A134, Y141, I142, E143, D154, R161, R164, Q165 | 1/17 | 5.9% | |
| 4DXA | Rap1 in complex with KRIT1 | Q25, H27, I36, E37, D38, S39, Y40, Q43, M67 | 1/9 | 11.1% | |
| 3T5G | Rheb in complex with PDE6D | T2, D57, G178, P179, G180 | 0/5 | 0.0% | |
| 2BOV | recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase | I139, P140, E143 | 1/3 | 33.3% | |
| 1UAD | Interaction between RalA and Sec5, a subunit of the sec6/8 complex | I36, G48, E49, T50, C51 | 1/5 | 20.0% |
From left to right: Functional group labels for clustered complexes; PDB Id codes of the Ras 3D complexes clustered with r.m.s. < 1.0; description of the Ras 3D complexes; positions involved in the binding site of the Ras complexes (those matching the DIRP specific positions are in bold); Number (Num.) and percentage (Ratio) of DIRP specific positions over all binding site positions. Positions numbering follows the human HRas protein sequence as reference.