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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ACYL-COA BINDING DOMAIN 4 COMPLEXED WITH STEAROYL-COA
 
Authors :  W. W. Yue, N. Shafqat, E. Ugochukwu, P. Savitsky, C. Johansson, E. Salah, A. K. Roos, A. Chaikuad, F. Von Delft, C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Date :  30 Apr 09  (Deposition) - 28 Jul 09  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Alternative Splicing, Fatty Acid Metabolism, Lipid Transport, Acyl-Coa Binding, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Shafqat, W. W. Yue, U. Oppermann
Crystal Structure Of Human Acyl-Coa Binding Domain 4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 4
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System VectorPNIC28-BSA4
    FragmentACYL-COA BINDING DOMAIN, RESIDUES 7-110
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2ST96Ligand/IonSTEAROYL-COENZYME A
3STE6Ligand/IonSTEARIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1COA-1Ligand/IonCOENZYME A
2ST91Ligand/IonSTEAROYL-COENZYME A
3STE1Ligand/IonSTEARIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1COA-1Ligand/IonCOENZYME A
2ST91Ligand/IonSTEAROYL-COENZYME A
3STE1Ligand/IonSTEARIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1COA-1Ligand/IonCOENZYME A
2ST91Ligand/IonSTEAROYL-COENZYME A
3STE1Ligand/IonSTEARIC ACID
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2ST91Ligand/IonSTEAROYL-COENZYME A
3STE1Ligand/IonSTEARIC ACID
Biological Unit 5 (3, 3)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2ST91Ligand/IonSTEAROYL-COENZYME A
3STE1Ligand/IonSTEARIC ACID
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
1COA-1Ligand/IonCOENZYME A
2ST91Ligand/IonSTEAROYL-COENZYME A
3STE1Ligand/IonSTEARIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:19 , PRO A:30 , TYR A:32 , ST9 A:901BINDING SITE FOR RESIDUE STE A 801
02AC2SOFTWAREVAL A:16 , ILE A:19 , GLN A:20 , LEU A:22 , PRO A:23 , LYS A:24 , GLY A:26 , SER A:27 , TYR A:28 , PRO A:30 , PHE A:38 , TYR A:39 , TYR A:42 , LYS A:43 , LYS A:65 , TYR A:84 , STE A:801 , HOH A:2001BINDING SITE FOR RESIDUE ST9 A 901
03AC3SOFTWAREPHE B:38 , TYR B:64 , ST9 B:901BINDING SITE FOR RESIDUE STE B 801
04AC4SOFTWAREVAL B:16 , ILE B:19 , GLN B:20 , LEU B:22 , PRO B:23 , SER B:27 , TYR B:28 , PRO B:30 , PHE B:38 , TYR B:39 , TYR B:42 , LYS B:43 , LYS B:65 , TYR B:84 , VAL B:91 , STE B:801BINDING SITE FOR RESIDUE ST9 B 901
05AC5SOFTWARELEU C:22 , MET C:35 , PHE C:38 , TYR C:64 , ST9 C:901BINDING SITE FOR RESIDUE STE C 801
06AC6SOFTWAREVAL C:16 , ILE C:19 , GLN C:20 , PRO C:23 , LYS C:24 , ASN C:25 , GLY C:26 , SER C:27 , TYR C:28 , PRO C:30 , PHE C:38 , TYR C:39 , TYR C:42 , LYS C:43 , LYS C:65 , TYR C:84 , STE C:801BINDING SITE FOR RESIDUE ST9 C 901
07AC7SOFTWAREILE D:19 , LEU D:22 , PHE D:38 , VAL D:91 , ST9 D:901BINDING SITE FOR RESIDUE STE D 801
08AC8SOFTWAREVAL D:16 , ILE D:19 , GLN D:20 , LEU D:22 , PRO D:23 , LYS D:24 , GLY D:26 , SER D:27 , TYR D:28 , PHE D:38 , TYR D:39 , TYR D:42 , LYS D:43 , LYS D:65 , TYR D:84 , STE D:801BINDING SITE FOR RESIDUE ST9 D 901
09AC9SOFTWAREPHE E:38 , TYR E:64 , LYS E:65 , ST9 E:901BINDING SITE FOR RESIDUE STE E 801
10BC1SOFTWAREVAL E:16 , ILE E:19 , GLN E:20 , PRO E:23 , SER E:27 , TYR E:28 , PRO E:30 , PHE E:38 , TYR E:39 , TYR E:42 , LYS E:43 , LYS E:65 , TYR E:84 , MET E:88 , VAL E:91 , ILE E:96 , STE E:801 , GLN F:11 , ALA F:15 , ILE F:85 , MET F:88 , LYS F:89 , ST9 F:901BINDING SITE FOR RESIDUE ST9 E 901
11BC2SOFTWAREPRO F:30 , TYR F:32 , MET F:35 , LEU F:36 , PHE F:38 , LYS F:65 , ST9 F:901BINDING SITE FOR RESIDUE STE F 801
12BC3SOFTWAREMET E:88 , LYS E:89 , ALA E:92 , ST9 E:901 , VAL F:16 , ILE F:19 , GLN F:20 , PRO F:23 , LYS F:24 , GLY F:26 , SER F:27 , TYR F:28 , PHE F:38 , TYR F:39 , TYR F:42 , LYS F:43 , LYS F:65 , TYR F:84 , STE F:801BINDING SITE FOR RESIDUE ST9 F 901
13BC4SOFTWARELYS B:74 , HOH B:2023 , ARG D:54 , HOH D:2006 , HOH D:2011 , ARG F:54 , ARG F:63 , TYR F:64BINDING SITE FOR RESIDUE COA D1099
14BC5SOFTWAREARG A:54 , ARG A:63 , TYR A:64 , ARG B:63 , TYR B:64 , LYS C:74 , ARG E:54 , ARG E:63BINDING SITE FOR RESIDUE COA E1099

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WH5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln B:9 -Lys B:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WH5)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  6A:30-48
B:30-48
C:30-48
D:30-48
E:30-48
F:30-48
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  1A:30-48
-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  1-
B:30-48
-
-
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  1-
-
C:30-48
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  1-
-
-
D:30-48
-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  1-
-
-
-
E:30-48
-
Biological Unit 6 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACB_1PS00880 Acyl-CoA-binding (ACB) domain signature.ACBD4_HUMAN34-52
 
 
 
 
 
  1-
-
-
-
-
F:30-48

(-) Exons   (0, 0)

(no "Exon" information available for 2WH5)

(-) 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:90
 aligned with ACBD4_HUMAN | Q8NC06 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:90
                                    22        32        42        52        62        72        82        92       102
          ACBD4_HUMAN    13 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVIDT 102
               SCOP domains d2wh5a_ A: automated matches                                                               SCOP domains
               CATH domains 2wh5A00 A:9-98  [code=1.20.80.10, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------ACB_1  PDB: A:30-48-------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2wh5 A   9 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVIDT  98
                                    18        28        38        48        58        68        78        88        98

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with ACBD4_HUMAN | Q8NC06 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:89
                                    22        32        42        52        62        72        82        92         
          ACBD4_HUMAN    13 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID 101
               SCOP domains d2wh5b_ B: automated matches                                                              SCOP domains
               CATH domains 2wh5B00 B:9-97  [code=1.20.80.10, no name defined]                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------ACB_1  PDB: B:30-48------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2wh5 B   9 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID  97
                                    18        28        38        48        58        68        78        88         

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with ACBD4_HUMAN | Q8NC06 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:90
                                    22        32        42        52        62        72        82        92       102
          ACBD4_HUMAN    13 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVIDT 102
               SCOP domains d2wh5c_ C: automated matches                                                               SCOP domains
               CATH domains 2wh5C00 C:9-98  [code=1.20.80.10, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------ACB_1  PDB: C:30-48-------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2wh5 C   9 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVIDT  98
                                    18        28        38        48        58        68        78        88        98

Chain D from PDB  Type:PROTEIN  Length:89
 aligned with ACBD4_HUMAN | Q8NC06 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:89
                                    22        32        42        52        62        72        82        92         
          ACBD4_HUMAN    13 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID 101
               SCOP domains d2wh5d_ D: automated matches                                                              SCOP domains
               CATH domains 2wh5D00 D:9-97  [code=1.20.80.10, no name defined]                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------ACB_1  PDB: D:30-48------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2wh5 D   9 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID  97
                                    18        28        38        48        58        68        78        88         

Chain E from PDB  Type:PROTEIN  Length:89
 aligned with ACBD4_HUMAN | Q8NC06 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:89
                                    22        32        42        52        62        72        82        92         
          ACBD4_HUMAN    13 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID 101
               SCOP domains d2wh5e_ E: automated matches                                                              SCOP domains
               CATH domains 2wh5E00 E:9-97  [code=1.20.80.10, no name defined]                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------ACB_1  PDB: E:30-48------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2wh5 E   9 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID  97
                                    18        28        38        48        58        68        78        88         

Chain F from PDB  Type:PROTEIN  Length:89
 aligned with ACBD4_HUMAN | Q8NC06 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:89
                                    22        32        42        52        62        72        82        92         
          ACBD4_HUMAN    13 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID 101
               SCOP domains d2wh5f_ F: automated matches                                                              SCOP domains
               CATH domains 2wh5F00 F:9-97  [code=1.20.80.10, no name defined]                                        CATH domains
           Pfam domains (1) ACBP-2wh5F01 F:9-96                                                                     - Pfam domains (1)
           Pfam domains (2) ACBP-2wh5F02 F:9-96                                                                     - Pfam domains (2)
           Pfam domains (3) ACBP-2wh5F03 F:9-96                                                                     - Pfam domains (3)
           Pfam domains (4) ACBP-2wh5F04 F:9-96                                                                     - Pfam domains (4)
           Pfam domains (5) ACBP-2wh5F05 F:9-96                                                                     - Pfam domains (5)
           Pfam domains (6) ACBP-2wh5F06 F:9-96                                                                     - Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------ACB_1  PDB: F:30-48------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2wh5 F   9 QKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLVAQKVID  97
                                    18        28        38        48        58        68        78        88         

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (ACBD4_HUMAN | Q8NC06)
molecular function
    GO:0000062    fatty-acyl-CoA binding    Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

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(no "Entries Sharing at Least One Protein Chain" available for 2WH5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WH5)