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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN P21-ACTIVATED KINASE 4
 
Authors :  J. E. Debreczeni, G. Bunkoczi, J. Eswaran, P. Filippakopoulos, S. Das, O. Fedorov, M. Sundstrom, C. Arrowsmith, A. Edwards, F. Von Delft, S. Knapp
Date :  23 Jun 05  (Deposition) - 14 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Kinase, Ste20, Pak4, Atp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Eswaran, W. H. Lee, J. E. Debreczeni, P. Filippakopoulos, A. Turnbull, O. Fedorov, S. W. Deacon, J. R. Peterson, S. Knapp
Crystal Structures Of The P21-Activated Kinases Pak4, Pak5, And Pak6 Reveal Catalytic Domain Plasticity Of Active Group Ii Paks.
Structure V. 15 201 2007
PubMed-ID: 17292838  |  Reference-DOI: 10.1016/J.STR.2007.01.001

(-) Compounds

Molecule 1 - P21-ACTIVATED KINASE 4
    ChainsA, B
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6B-C001
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR (PHAGE RESISTANT)
    Expression System VectorPGEX6B
    FragmentKINASE DOMAIN, RESIDUES 300-591
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPHOSPHORYLATION ON SER 474 A AND SER 474 B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 2BVA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PAK4_HUMAN327-351
 
  2A:327-351
B:327-351
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PAK4_HUMAN327-351
 
  1A:327-351
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PAK4_HUMAN327-351
 
  1-
B:327-351

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003604422ENSE00001510615chr19:39659251-39659480230PAK4_HUMAN-00--
1.3bENST000003604423bENSE00000882572chr19:39660172-39660397226PAK4_HUMAN1-68680--
1.4ENST000003604424ENSE00001242921chr19:39663558-39664016459PAK4_HUMAN69-2211530--
1.5ENST000003604425ENSE00000882573chr19:39664216-39664650435PAK4_HUMAN222-3661452A:300-366 (gaps)
B:301-366 (gaps)
67
66
1.6ENST000003604426ENSE00001777324chr19:39665571-39665704134PAK4_HUMAN367-411452A:367-411
B:367-411
45
45
1.7ENST000003604427ENSE00000882575chr19:39665952-39666078127PAK4_HUMAN411-453432A:411-453
B:411-453
43
43
1.8ENST000003604428ENSE00000704690chr19:39667230-39667355126PAK4_HUMAN454-495422A:454-495 (gaps)
B:454-495 (gaps)
42
42
1.9ENST000003604429ENSE00000882577chr19:39668315-39668449135PAK4_HUMAN496-540452A:496-540
B:496-540
45
45
1.10ENST0000036044210ENSE00001296813chr19:39669064-39670046983PAK4_HUMAN541-591512A:541-587
B:541-587
47
47

(-) 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:273
 aligned with PAK4_HUMAN | O96013 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:288
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579        
           PAK4_HUMAN   300 SHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQ 587
               SCOP domains d2bvaa_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2bvaA01 A:300-397 Phosphoryla     se Kinase; domain 1                                             2bvaA02 A:398-587 Transferase(Phosphotransferase) domain 1                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh..................-----....................--------.hhhhhhhhhh........eeeeee....eeeee.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........--..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------PROTEIN_KINASE_ATP       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:300-366 (gaps) UniProt: 222-366 [INCOMPLETE]      Exon 1.6  PDB: A:367-411 UniProt: 367-411    ------------------------------------------Exon 1.8  PDB: A:454-495 (gaps)           Exon 1.9  PDB: A:496-540 UniProt: 496-540    Exon 1.10  PDB: A:541-587 UniProt: 541-591      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:411-453 UniProt: 411-453  -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2bva A 300 SHEQFRAALQLVVDPGDPRSYLDNFIKIG-----IVCIATVRSSGKLVAVKKMD--------LLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQV--EVPRRKsLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQ 587
                                   309       319        |-    |  339       349   |     -  |    369       379       389       399       409       419       429       439       449       459     | 469    |  479       489       499       509       519       529       539       549       559       569       579        
                                                      328   334                353      362                                                                                                    465  |     |                                                                                                                 
                                                                                                                                                                                                  468     |                                                                                                                 
                                                                                                                                                                                                        474-SEP                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with PAK4_HUMAN | O96013 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:287
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       
           PAK4_HUMAN   301 HEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQ 587
               SCOP domains d2bvab_ B: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2bvaB01 B:301-397 Phosphorylas   e Kinase; domain 1                                              2bvaB02 B:398-587 Transferase(Phosphotransferase) domain 1                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.....................---....ee......eeee.....-------hhhhhhhhhh.........eeeeee....eeeee......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.--..........hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh............hhhhhhhhh...........hhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------PROTEIN_KINASE_ATP       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:301-366 (gaps) UniProt: 222-366 [INCOMPLETE]     Exon 1.6  PDB: B:367-411 UniProt: 367-411    ------------------------------------------Exon 1.8  PDB: B:454-495 (gaps)           Exon 1.9  PDB: B:496-540 UniProt: 496-540    Exon 1.10  PDB: B:541-587 UniProt: 541-591      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:411-453 UniProt: 411-453  -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2bva B 301 HEQFRAALQLVVDPGDPRSYLDNFIKIGEG---IVCIATVRSSGKLVAVKKMDL-------LLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQV--EVPRRKsLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQ 587
                                   310       320       330   |   340       350   |     - |     370       380       390       400       410       420       430       440       450       460    |  470   |   480       490       500       510       520       530       540       550       560       570       580       
                                                       330 334                 354     362                                                                                                    465  |     |                                                                                                                 
                                                                                                                                                                                                 468     |                                                                                                                 
                                                                                                                                                                                                       474-SEP                                                                                                             

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAK4_HUMAN | O96013)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0004702    signal transducer, downstream of receptor, with serine/threonine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0060996    dendritic spine development    The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PAK4_HUMAN | O960132cdz 2j0i 2ov2 2q0n 2x4z 4app 4fie 4fif 4fig 4fih 4fii 4fij 4jdh 4jdi 4jdj 4jdk 4l67 4njd 4o0v 4o0x 4o0y 4xbr 4xbu 5bms 5i0b

(-) Related Entries Specified in the PDB File

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