triangle PDBeMotif: 4gdk  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
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Classification protein binding    | release date: Tue, Jul 31, 2012
Title crystal structure of human atg12~atg5 conjugate in complex w terminal fragment of atg16l1
Authors C.OTOMO, G.TAKAESU, T.OTOMO, Z.METLAGEL
Method X-RAY DIFFRACTION (resolution: 2.70Å)
PDBe Citation   
Small molecules:    search NA NA binding statistics NA
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chains A,D sequence:
GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKL
VLHYCKSQAWG
Chains B,E sequence:
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWH
YPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQND
RFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI
HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD
Chains C,F sequence:
SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain A : UBIQUITIN-LIKE PROTEIN ATG12
member of: GENE3D:searchG3DSA_3.10.20.90PANTHER:searchPTHR13385PFAM:searchPF04110SUPERFAMILY:searchSSF54236UniProt:searchO94817
sec str:  ...eeeeeeee..........eeeee...hhhhhhhhhhhhh........eeee..........hhhhhhhhhh...eeeeeee......
sequence :  ..KKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCKSQAWG
seq num:  ..53        63        73        83        93        103       113       123       133     
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..|                | |   |  |            | ||  |      ^***  |  |   |  |  |                
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..*                ^**   |  |            | ||  |       | |  |  |   |  |  |                
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..                 | |   |  |            | ||  |       | |  |  |   ^***  |                
search RasMol script viewer Motif-ligand binding stats  nest ..                 | |   |  |            ***|  |       ***  |  |      |  |                
search RasMol script viewer Motif-ligand binding stats  niche ..                 ***   ****               ****            ****      ****                

chain B : AUTOPHAGY PROTEIN 5
member of: PANTHER:searchPTHR13040/searchPTHR13040_SF2PFAM:searchPF04106UniProt:searchQ9H1Y0
JMol viewer RasMol script viewer  NA 301B  ..                                                                                            * * *                                                                                                                                 ..NA ..                                         
sec str:  ...hhhhhhhhhh.eeeeeeee............eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeee..ee.....hhhhhhhhhhh.....eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh............eeee.......ee..............hhhhhhhhhhhhhh.... ...eeee..........hhhhhhhhh......eeeeeee....
sequence :  ..DDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAID... ..KNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD
seq num:  ..3         13        23        33        43        53        63        73        83        93        103       113       123       133       143       153       163       173       183       193       203       213       223   ... ..235       245       255       265        
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..        |  |        |  | | ||    |        |   | |     |  ||| ||      |  |  |  |      |  || |    ^*** | || |  |    | |                 | ||||  |             | |         |  | |  |           || |||       | |  |||  || ||      |  |..PS00001..           |  |     ||  |  | |           
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..        |  |        |  | ^**|    |        |   ^**     |  ||| ||      |  |  |  |      |  || |         | || |  |    | |                 | ||||  |             | |         |  | |  |           || ^**       | |  |||  || ||      |  |..PS00005..           |  |     ||  |  | |           
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..        |  |        |  | ^***    |        |   |       |  ||| ||      |  |  |  |      |  || |         | ^***  |    | |                 | ||||  |             | |         |  | |  |           |^***|       | |  |||  ^***|      ^***..PS00006..           |  |     ||  ^*** |           
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..        |  |        |  |   ******^        |   |       |  ||| ||      |  |  |  |      |  || |         |  | |  |    | |                 | ||||  |             | |         |  | |  |           |  | |       | |  |||  ||  |          ..PS00007..           |  |     ||  |  | |           
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..        |  |        |  |                  |   |       |  ||| ||      |  |  |  |      |  || |         |  | |  |    | |                 | ||||  |             | |         |  | |  |           |  | |       | |  |^*****  |          ..PS00008..           |  |     ||  |  | |           
search RasMol script viewer Motif-ligand binding stats  asxturn ..        |  |        |  |                  |   |       |  ||| ||      |  |  |  |      |  || |         |  | |  |    | |                 | ||||  |             | |         |  | |  |           |  | |       | |  | |  |   |          ..asxturn..           |  |     ||  |  ***           
search RasMol script viewer Motif-ligand binding stats  betaturn ..        |  |        |  |                  |   |       |  |****|      ****  |  |      |  || |         |  | |  |    | |                 ****||  |             | |         |  | |  |           |  | |       | |  | |  |   |          ..betaturn..           |  |     ||  |  | |           
search RasMol script viewer Motif-ligand binding stats  nest ..        |  |        |  |                  |   |       |  | |  |            |  |      |  || |         |  | |  |    | |                 *****|  |             ***         |  | |  |           |  | |       | |  ***  |   |          ..nest..           |  |     ||  |  ***           
search RasMol script viewer Motif-ligand binding stats  niche ..        ****        ****                  |   |       **** ****            ****      |  ****         **** ****    | |                      ****                         **** ****           ******       ***       |   |          ..niche..           ****     |****                
search RasMol script viewer Motif-ligand binding stats  stmotif ..                                          |   |                                      |   |                        | |                                                                                              *****          ..stmotif..                    |   |                
search RasMol script viewer Motif-ligand binding stats  ststaple ..                                          *****                                      *****                        | |                                                                                                             ..ststaple..                    *****                
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                                  ***                                                                                                             ..stturn..                                         

chain C : AUTOPHAGY-RELATED PROTEIN 16-1
member of: PANTHER:searchPTHR19878/searchPTHR19878_SF3PFAM:searchPF08614UniProt:searchQ676U5
sec str:  ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.
sequence :  ..MPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
seq num:  ..10        20        30        40  

chain D : UBIQUITIN-LIKE PROTEIN ATG12
member of: GENE3D:searchG3DSA_3.10.20.90PANTHER:searchPTHR13385PFAM:searchPF04110SUPERFAMILY:searchSSF54236UniProt:searchO94817
sec str:  ...eeeeeee..........eeee....hhhhhhhhhhhhh........eeee..........hhhhhhhhhh....eeeeee......
sequence :  ..KIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCKSQAWG
seq num:  ..54        64        74        84        94        104       114       124       134    
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..                | |   |  ||   |       | ||  |      ^***  |  |   |  |  |                
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..                ^**   |  ||   |       | ||  |            |  |   |  |  |                
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..                | |   |  ||   |       | ||  |            |  |   ^***  |                
search RasMol script viewer Motif-ligand binding stats  betaturn ..                | |   |  ||   |       | ||  |            ****      |  |                
search RasMol script viewer Motif-ligand binding stats  nest ..                | |   |  ||   |       ***|  |            |  |      |  |                
search RasMol script viewer Motif-ligand binding stats  niche ..                ***   ****|   |          ****            ****      ****                
search RasMol script viewer Motif-ligand binding stats  stmotif ..                          *****                                                        

chain E : AUTOPHAGY PROTEIN 5
member of: PANTHER:searchPTHR13040/searchPTHR13040_SF2PFAM:searchPF04106UniProt:searchQ9H1Y0
JMol viewer RasMol script viewer  NA 301E  ..                                                                                            * * *                                                                                                                                ..NA ..                                        
sec str:  ...hhhhhhhhhh.eeeeeeee............eeeeee...hhhhhhhhhhhhhhh..........eeee..ee.....hhhhhhhhhh......eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhh............eeeee......................hhhhhhhhhh....... ...eeee..........hhhhhhhhh......eeeeeee...
sequence :  ..DDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAI... ..KNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPT
seq num:  ..3         13        23        33        43        53        63        73        83        93        103       113       123       133       143       153       163       173       183       193       203       213       223  ... ..235       245       255       265       
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..        |  |        |  | | ||    |        |   | |     |  ||| ||            |  |      |  || |    ^***   |  |  |                        | | ||  |             | |         |  | |  |           || |||            |||  || |       |  ..PS00001..           |  |     ||  || |||          
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..        |  |        |  | ^**|    |        |   ^**     |  ||| ||            |  |      |  || |           |  |  |                        | | ||  |             | |         |  | |  |           || ^**            |||  || |       |  ..PS00005..           |  |     ||  || |||          
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..        |  |        |  | ^***    |        |   |       |  ||| ||            |  |      |  || |           ^***  |                        | | ||  |             | |         |  | |  |           |^***             |||  ^***       ^**..PS00006..           |  |     ||  ^***||          
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..        |  |        |  |   ******^        |   |       |  ||| ||            |  |      |  || |              |  |                        | | ||  |             | |         |  | |  |           |  |              |||   |            ..PS00007..           |  |     ||  || |||          
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..        |  |        |  |                  |   |       |  ||| ||            |  |      |  || |              |  |                        | | ||  |             | |         |  | |  |           |  |              |^*****            ..PS00008..           |  |     ||  || |||          
search RasMol script viewer Motif-ligand binding stats  asxturn ..        |  |        |  |                  |   |       |  ||| ||            |  |      |  || |              |  |                        | | ||  |             | |         |  | |  |           |  |              | |                ..asxturn..           |  |     ||  || ***          
search RasMol script viewer Motif-ligand binding stats  betabulgeloop ..        |  |        |  |                  |   |       |  ||| ||            |  |      |  || |              |  |                        | | ||  |             | |         |  | |  |           |  |              | |                ..betabulgeloop..           |  |     ||  |*****          
search RasMol script viewer Motif-ligand binding stats  betaturn ..        |  |        |  |                  |   |       |  |****|            |  |      |  ****              |  |                        | | ||  |             | |         |  | |  |           |  |              | |                ..betaturn..           |  |     ||  |****|          
search RasMol script viewer Motif-ligand binding stats  nest ..        |  |        |  |                  |   |       |  | |  |            |  |      |  || |              |  |                        *****|  |             ***         |  | |  |           |  |              ***                ..nest..           |  |     ||  |  ***          
search RasMol script viewer Motif-ligand binding stats  niche ..        ****        ****                  |   |       **** ****            ****      |  ****              ****                             ****                         **** ****           ****                                 ..niche..           ****     |****               
search RasMol script viewer Motif-ligand binding stats  ststaple ..                                          *****                                      *****                                                                                                                                       ..ststaple..                    *****               

chain F : AUTOPHAGY-RELATED PROTEIN 16-1
member of: PANTHER:searchPTHR19878/searchPTHR19878_SF3PFAM:searchPF08614UniProt:searchQ676U5
sec str:  ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.
sequence :  ..HMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL
seq num:  ..9         19        29        39   

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