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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TIM9 TIM10 HEXAMERIC COMPLEX
 
Authors :  C. T. Webb, M. A. Gorman, M. Lazarus, M. T. Ryan, J. M. Gulbis
Date :  23 May 05  (Deposition) - 04 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein Transport, Tim9, Tim10, Mitochondrial Protein Import, Tim Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. T. Webb, M. A. Gorman, M. Lazarou, M. T. Ryan, J. M. Gulbis
Crystal Structure Of The Mitochondrial Chaperone Tim9*10 Reveals A Six-Bladed Alpha-Propeller.
Mol. Cell V. 21 123 2006
PubMed-ID: 16387659  |  Reference-DOI: 10.1016/J.MOLCEL.2005.11.010

(-) Compounds

Molecule 1 - MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM9 A
    ChainsA, C, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX 4T2
    Expression System StrainORIGAMI DE3 PLYSS
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10
    ChainsB, D, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX 4T2
    Expression System StrainORIGAMI DE3 PLYSS
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 19)

Asymmetric/Biological Unit (1, 19)
No.NameCountTypeFull Name
1MSE19Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2BSK)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:52
2A:32 -A:48
3B:29 -B:54
4B:33 -B:50
5C:28 -C:52
6C:32 -C:48
7D:29 -D:54
8D:33 -D:50
9E:28 -E:52
10E:32 -E:48
11F:29 -F:54
12F:33 -F:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BSK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BSK)

(-) Exons   (5, 15)

Asymmetric/Biological Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002572451bENSE00001027295chr11:57298238-57298131108TIM10_HUMAN-00--
1.2bENST000002572452bENSE00000916207chr11:57297707-57297592116TIM10_HUMAN1-24243B:13-24
D:1-24
F:10-24
12
24
15
1.3cENST000002572453cENSE00000916206chr11:57296391-57295936456TIM10_HUMAN24-90673B:24-77
D:24-90
F:24-73
54
67
50

2.1ENST000003951591ENSE00001389910chr14:58894232-58894110123TIM9_HUMAN-00--
2.2bENST000003951592bENSE00001520759chr14:58893960-58893767194TIM9_HUMAN-00--
2.3bENST000003951593bENSE00001520757chr14:58890808-5889072683TIM9_HUMAN-00--
2.4bENST000003951594bENSE00001374830chr14:58878689-5887862565TIM9_HUMAN1-13133A:13-13
C:9-13
E:13-13
1
5
1
2.5ENST000003951595ENSE00000658069chr14:58877656-5887756196TIM9_HUMAN14-45323A:14-45
C:14-45
E:14-45
32
32
32
2.6bENST000003951596bENSE00001520754chr14:58875886-58875214673TIM9_HUMAN46-89443A:46-85
C:46-87
E:46-75
40
42
30

(-) Sequences/Alignments

Asymmetric/Biological 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:73
 aligned with TIM9_HUMAN | Q9Y5J7 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:73
                                    22        32        42        52        62        72        82   
            TIM9_HUMAN   13 QFKEFLGTYNKLTETCFLDCVKDFTTREVKPEETTCSEHCLQKYLKMTQRISMRFQEYHIQQNEALAAKAGLL 85
               SCOP domains d2bska1 A:13-85                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
               Transcript 2 2Exon 2.5  PDB: A:14-45          Exon 2.6b  PDB: A:46-85 UniProt: 46-89   Transcript 2
                  2bsk A 13 QFKEFLGTYNKLTETCFLDCVKDFTTREVKPEETTCSEHCLQKYLKMTQRISMRFQEYHIQQNEALAAKAGLL 85
                                    22        32        42        52        62        72        82   

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with TIM10_HUMAN | P62072 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:65
                                    22        32        42        52        62        72     
           TIM10_HUMAN   13 LEVEMMADMYNRMTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERMGKKLTELSMQDE 77
               SCOP domains d2bskb1 B:13-77                                                   SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b   ----------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.3c  PDB: B:24-77 UniProt: 24-90 [INCOMPLETE]    Transcript 1 (2)
                  2bsk B 13 LEVEmmADmYNRmTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERmGKKLTELSmQDE 77
                                ||  22  |     32        42        52        62  |     72 |   
                                ||  |   |                                      65-MSE   74-MSE
                               17-MSE   |                                                    
                                18-MSE  |                                                    
                                   21-MSE                                                    
                                       25-MSE                                                

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with TIM9_HUMAN | Q9Y5J7 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:79
                                    18        28        38        48        58        68        78         
            TIM9_HUMAN    9 DQIKQFKEFLGTYNKLTETCFLDCVKDFTTREVKPEETTCSEHCLQKYLKMTQRISMRFQEYHIQQNEALAAKAGLLGQ 87
               SCOP domains ----d2bskc1 C:13-85                                                          -- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
               Transcript 2 2.4b Exon 2.5  PDB: C:14-45          Exon 2.6b  PDB: C:46-87 UniProt: 46-89     Transcript 2
                  2bsk C  9 DQIKQFKEFLGTYNKLTETCFLDCVKDFTTREVKPEETTCSEHCLQKYLKMTQRISMRFQEYHIQQNEALAAKAGLLGQ 87
                                    18        28        38        48        58        68        78         

Chain D from PDB  Type:PROTEIN  Length:90
 aligned with TIM10_HUMAN | P62072 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:90
                                    10        20        30        40        50        60        70        80        90
           TIM10_HUMAN    1 MDPLRAQQLAAELEVEMMADMYNRMTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERMGKKLTELSMQDEELMKRVQQSSGPA 90
               SCOP domains ------------d2bskd1 D:13-77                                                  ------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: D:1-24  ------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.3c  PDB: D:24-90 UniProt: 24-90                              Transcript 1 (2)
                  2bsk D  1 mDPLRAQQLAAELEVEmmADmYNRmTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERmGKKLTELSmQDEELmKRVQQSSGPA 90
                            |       10      ||20|   |   30        40        50        60    |   70   |    80        90
                            |              17-MSE   |                                      65-MSE   74-MSE |          
                            1-MSE           18-MSE  |                                                     80-MSE      
                                               21-MSE                                                                 
                                                   25-MSE                                                             

Chain E from PDB  Type:PROTEIN  Length:63
 aligned with TIM9_HUMAN | Q9Y5J7 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:63
                                    22        32        42        52        62        72   
            TIM9_HUMAN   13 QFKEFLGTYNKLTETCFLDCVKDFTTREVKPEETTCSEHCLQKYLKMTQRISMRFQEYHIQQN 75
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
               Transcript 2 2Exon 2.5  PDB: E:14-45          Exon 2.6b  PDB: E:46-75        Transcript 2
                  2bsk E 13 QFKEFLGTYNKLTETCFLDCVKDFTTREVKPEETTCSEHCLQKYLKMTQRISMRFQEYHIQQN 75
                                    22        32        42        52        62        72   

Chain F from PDB  Type:PROTEIN  Length:64
 aligned with TIM10_HUMAN | P62072 from UniProtKB/Swiss-Prot  Length:90

    Alignment length:64
                                    19        29        39        49        59        69    
           TIM10_HUMAN   10 AAELEVEMMADMYNRMTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERMGKKLTELS 73
               SCOP domains ---d2bskf1 F:13-73                                               SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b      ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.3c  PDB: F:24-73 UniProt: 24-90             Transcript 1 (2)
                  2bsk F 10 AAELEVEmmADmYNRmTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERmGKKLTELS 73
                                   |19 |   |  29        39        49        59     |  69    
                                  17-MSE   |                                      65-MSE    
                                   18-MSE  |                                                
                                      21-MSE                                                
                                          25-MSE                                            

   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  (2, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BSK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BSK)

(-) Gene Ontology  (20, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,E   (TIM9_HUMAN | Q9Y5J7)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0072321    chaperone-mediated protein transport    The directed movement of proteins into, out of or within a cell, or between cells, mediated by chaperone molecules that bind to the transported proteins.
    GO:0045039    protein import into mitochondrial inner membrane    The process comprising the import of proteins into the mitochondrion from outside the organelle and their insertion into the mitochondrial inner membrane. The translocase of the outer membrane complex mediates the passage of these proteins across the outer membrane, after which they are guided by either of two inner membrane translocase complexes into their final destination in the inner membrane.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0042721    mitochondrial inner membrane protein insertion complex    A multi-subunit complex embedded in the mitochondrial inner membrane that mediates insertion of carrier proteins into the inner membrane.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0042719    mitochondrial intermembrane space protein transporter complex    Soluble complex of the mitochondrial intermembrane space composed of various combinations of small Tim proteins; acts as a protein transporter to guide proteins to the Tim22 complex for insertion into the mitochondrial inner membrane.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain B,D,F   (TIM10_HUMAN | P62072)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0072321    chaperone-mediated protein transport    The directed movement of proteins into, out of or within a cell, or between cells, mediated by chaperone molecules that bind to the transported proteins.
    GO:0045039    protein import into mitochondrial inner membrane    The process comprising the import of proteins into the mitochondrion from outside the organelle and their insertion into the mitochondrial inner membrane. The translocase of the outer membrane complex mediates the passage of these proteins across the outer membrane, after which they are guided by either of two inner membrane translocase complexes into their final destination in the inner membrane.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005744    mitochondrial inner membrane presequence translocase complex    The protein transport machinery of the mitochondrial inner membrane that contains three essential Tim proteins: Tim17 and Tim23 are thought to build a preprotein translocation channel while Tim44 interacts transiently with the matrix heat-shock protein Hsp70 to form an ATP-driven import motor.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0042719    mitochondrial intermembrane space protein transporter complex    Soluble complex of the mitochondrial intermembrane space composed of various combinations of small Tim proteins; acts as a protein transporter to guide proteins to the Tim22 complex for insertion into the mitochondrial inner membrane.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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