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(-) Description

Title :  COMPLEX STRUCTURE OF BCL-XL AND MUTATED BIM BH3 DOMAIN
 
Authors :  N. C. Ha, J. S. Kim
Date :  04 Mar 15  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,F,G
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  F,G  (1x)
Keywords :  Bcl-Xl, Bim, Bh3, Complex, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. C. Ha, J. S. Kim
Complex Structure Of Bcl-Xl And Mutated Bim Bh3 Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BCL-2-LIKE PROTEIN 1
    Chains: A, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-196
    Gene: BCL2L1, BCL2L, BCLX
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: BCL2-L-1,APOPTOSIS REGULATOR BCL-X
 
Molecule 2 - BH3BIM
    Chains: B, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFG
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   FG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1AAR2Mod. Amino AcidARGININEAMIDE
2ACT3Ligand/IonACETATE ION
3CL3Ligand/IonCHLORIDE ION
4NLG2Mod. Amino AcidN-ACETYL-L-GLUTAMATE
5SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1AAR1Mod. Amino AcidARGININEAMIDE
2ACT2Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4NLG1Mod. Amino AcidN-ACETYL-L-GLUTAMATE
5SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1AAR1Mod. Amino AcidARGININEAMIDE
2ACT1Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4NLG1Mod. Amino AcidN-ACETYL-L-GLUTAMATE
5SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:100 , TYR A:101 , SEP B:14 , PHE B:15 , THR F:109 , HOH F:338binding site for residue ACT A 201
02AC2SOFTWAREASP A:107 , HOH A:301 , GLU B:7 , TYR F:22binding site for residue CL A 202
03AC3SOFTWAREARG A:132binding site for residue CL A 203
04AC4SOFTWARETHR A:109 , SER A:110 , HOH A:312 , ARG F:100 , TYR F:101 , SEP G:14 , PHE G:15binding site for residue ACT A 204
05AC5SOFTWAREASN F:136 , ARG F:139binding site for residue ACT F 201
06AC6SOFTWARETYR A:22 , HOH A:320 , ASP F:107 , GLU G:7binding site for residue CL F 202
07AC7SOFTWAREGLN F:111 , LEU F:112 , SER F:122 , GLN F:125 , VAL F:126 , ASN F:128 , TRP G:3 , ILE G:4 , ALA G:5 , GLN G:6binding site for Di-peptide NLG G 1 and ILE G 2
08AC8SOFTWAREARG A:102 , ACT A:204 , HOH A:312 , TYR F:101 , ASN F:136 , ARG F:139 , HOH F:303 , ARG G:9 , SER G:10 , ARG G:11 , GLY G:12 , PHE G:15 , ASN G:16 , ALA G:17 , TYR G:18 , HOH G:108binding site for Di-peptide ASP G 13 and SEP G 14
09AC9SOFTWAREARG A:102 , ACT A:204 , HOH A:312 , TYR F:101 , TYR F:195 , HOH F:303 , SER G:10 , ARG G:11 , GLY G:12 , ASP G:13 , ASN G:16 , ALA G:17 , TYR G:18 , TYR G:19binding site for Di-peptide SEP G 14 and PHE G 15
10AD1SOFTWARESER F:25 , GLN F:26 , PHE F:27 , SER F:28 , ASP F:29 , GLN F:160 , ASP F:193 , ASN G:16 , TYR G:18 , TYR G:19 , HOH G:102 , HOH G:107binding site for Di-peptide ALA G 20 and AAR G 21

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YK9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YK9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YK9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YK9)

(-) Exons   (0, 0)

(no "Exon" information available for 4YK9)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yk9 A   2 SQSNRELVVDFLSYKLSQKGYSWSQFSDVAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG 196
                                    11        21        84        94       104       114       124       134       144       154       164       174       184       194  
                                                       30|                                                                                                                
                                                        84                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 4yk9 B   1 xIWIAQELRSRGDsFNAYYAr  21
                            |       10   |    20|
                            1-NLG       14-SEP 21-AAR


Chain F from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yk9 F   2 SQSNRELVVDFLSYKLSQKGYSWSQFSDVAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG 196
                                    11        21        84        94       104       114       124       134       144       154       164       174       184       194  
                                                       30|                                                                                                                
                                                        84                                                                                                                


Chain G from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 4yk9 G   1 xIWIAQELRSRGDsFNAYYAr  21
                            |       10   |    20|
                            1-NLG       14-SEP 21-AAR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4YK9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YK9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YK9)

(-) Gene Ontology  (66, 66)

Asymmetric Unit(hide GO term definitions)

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        B2CL1_MOUSE | Q64373: 1pq0 1pq1 2bzw 3ihc 3ihd 3ihe 3ihf 3iig 3iih 3ilb 3ilc 4yj4 5c3g

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