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(-) Description

Title :  HUMAN MALT1 (CASPASE-IG3) IN COMPLEX WITH ACTIVITY BASED-PROBE
 
Authors :  F. Schlauderer, K. Lammens, K. P. Hopfner
Date :  21 Nov 12  (Deposition) - 09 Jul 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Eitelhuber, O. Vosyka, D. Nagel, M. Bognar, D. Lenze, K. Lammens, F. Schlauderer, D. Hlahla, K. P. Hopfner, G. Lenz, M. Hummel, S. H. Verhelst, D. Krappmann
Activity-Based Probes For Detection Of Active Malt1 Paracaspase In Immune Cells And Lymphomas.
Chem. Biol. V. 22 129 2015
PubMed-ID: 25556945  |  Reference-DOI: 10.1016/J.CHEMBIOL.2014.10.021

(-) Compounds

Molecule 1 - MUCOSA-ASSOCIATED LYMPHOID TISSUE LYMPHOMA TRANSLOCATION PROTEIN 1
    Chains: A, C
    EC Number: 3.4.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 339-719
    Gene: MALT1, MLT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MALT LYMPHOMA-ASSOCIATED TRANSLOCATION, PARACASPASE
 
Molecule 2 - TETRAPEPTIDE
    Chains: B, D
    Engineered: YES
    Other Details: SYNTHETIC PRODUCTION OF TETRAPEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
14AR2Mod. Amino AcidAMINO({(4S)-4-AMINO-6-[(2,6-DIMETHYLBENZOYL)OXY]-5-OXOHEXYL}AMINO)METHANIMINIUM
2ACT10Ligand/IonACETATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
14AR1Mod. Amino AcidAMINO({(4S)-4-AMINO-6-[(2,6-DIMETHYLBENZOYL)OXY]-5-OXOHEXYL}AMINO)METHANIMINIUM
2ACT5Ligand/IonACETATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
14AR1Mod. Amino AcidAMINO({(4S)-4-AMINO-6-[(2,6-DIMETHYLBENZOYL)OXY]-5-OXOHEXYL}AMINO)METHANIMINIUM
2ACT5Ligand/IonACETATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
14AR1Mod. Amino AcidAMINO({(4S)-4-AMINO-6-[(2,6-DIMETHYLBENZOYL)OXY]-5-OXOHEXYL}AMINO)METHANIMINIUM
2ACT5Ligand/IonACETATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:490 , GLN A:494 , GLU A:549 , ARG A:551 , ARG C:551BINDING SITE FOR RESIDUE ACT A 801
02AC2SOFTWAREGLU A:497 , PHE A:499BINDING SITE FOR RESIDUE ACT A 802
03AC3SOFTWAREARG A:392 , ACT A:804BINDING SITE FOR RESIDUE ACT A 803
04AC4SOFTWAREARG A:392 , CYS A:439 , LEU A:440 , CYS A:441 , ASN A:444 , ACT A:803BINDING SITE FOR RESIDUE ACT A 804
05AC5SOFTWAREHOH A:907 , ASP C:530 , GLU C:534BINDING SITE FOR RESIDUE ACT A 805
06AC6SOFTWAREARG C:392 , VAL C:395BINDING SITE FOR RESIDUE ACT C 801
07AC7SOFTWARETYR C:434 , ASP C:478BINDING SITE FOR RESIDUE ACT C 802
08AC8SOFTWAREGLU C:390 , ALA C:394 , GLN C:676BINDING SITE FOR RESIDUE ACT C 803
09AC9SOFTWAREMET C:338 , ASP C:522 , HOH C:953BINDING SITE FOR RESIDUE ACT C 804
10BC1SOFTWAREGLU C:397 , GLN C:579 , LEU C:715BINDING SITE FOR RESIDUE ACT C 805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I1P)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:432 -Pro A:433
2Asn C:432 -Pro C:433
3Gly C:505 -Leu C:506

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I1P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I1P)

(-) Exons   (0, 0)

(no "Exon" information available for 4I1P)

(-) 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:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee...........hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh....eeeeeee..eeee..eeee.........hhhhheehhhhhhhhhhh...eeeeeee.......................eeeee........ee........hhhhhhhh.......hhhhhhhhhhhhhhh..........eeee.................hhhhhhhhhhhhhhhh....eeee.....eeeeeeeeee..eeeeeeeeee....eeeeeeeee..hhhhh.hhhhh...hhhhhh............eeeee.hhhhh...eeeeeeeeeee......eeeeeeeeee.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i1p A 338 MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSSLSEKRALTDPIQGTEYSAESLVRNLQWAKAHELPESMCLKFDCGVQIQLGFAAEFSNVMIIYTSIVYKPPEIIMCDAYVTDFPLDLDIDPKDANKGTPEETGSYLVSKDLPKHCLYTRLSSLQKLKEHLVFTVCLSYQYSGLEDTVEDKQEVNVGKPLIAKLD 716
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707         


Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4i1p B   0 ALRSr   4
                                |
                                4-4AR


Chain C from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee...........hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.....eeeeeee..eeee..eeee.........hhhhheehhhhhhhhhhh...eeeeeee.......................eeeee........ee........hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....eeee.................hhhhhhhhhhhhhhhh....eeee.....eeeeeeeeee..eeeeeeeeee....eeeeeeeee..hhhhh..........hhhhh............eeeee.hhhhh....eeeeeeeeee......eeeeeeee...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i1p C 338 MLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSSLSEKRALTDPIQGTEYSAESLVRNLQWAKAHELPESMCLKFDCGVQIQLGFAAEFSNVMIIYTSIVYKPPEIIMCDAYVTDFPLDLDIDPKDANKGTPEETGSYLVSKDLPKHCLYTRLSSLQKLKEHLVFTVCLSYQYSGLEDTVEDKQEVNVGKPLIAKLDM 717
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4i1p D   0 ALRSr   4
                                |
                                4-4AR
   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 4I1P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I1P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I1P)

(-) Gene Ontology  (41, 41)

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        MALT1_HUMAN | Q9UDY8: 2g7r 3bfo 3k0w 3uo8 3uoa 3v4o 3v55 4i1r

(-) Related Entries Specified in the PDB File

4i1r