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(-) Description

Title :  MT1-MMP:FAB COMPLEX (FORM II)
 
Authors :  H. Rozenberg, Y. Udi, I. Sagi
Date :  07 Mar 14  (Deposition) - 17 Dec 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,H,L,M
Keywords :  Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Udi, M. Grossman, I. Solomonov, O. Dym, H. Rozenberg, V. Moreno, P. Cuniasse, V. Dive, A. G. Arroyo, I. Sagi
Inhibition Mechanism Of Membrane Metalloprotease By An Exosite-Swiveling Conformational Antibody.
Structure V. 23 104 2015
PubMed-ID: 25482542  |  Reference-DOI: 10.1016/J.STR.2014.10.012

(-) Compounds

Molecule 1 - HEAVY CHAIN FAB FRAGMENT OF ANTIBODY LEM-2/15
    Chains: A, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - LIGHT CHAIN FAB FRAGMENT OF ANTIBODY LEM-2/15
    Chains: B, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - MATRIX METALLOPROTEINASE-14
    Chains: C, M
    EC Number: 3.4.24.80
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETR3A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: MT1-MMP V-B LOOP
    Gene: MMP14
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MMP-14, MMP-X1, MEMBRANE-TYPE MATRIX METALLOPROTEINASE 1, MTMMP1, MEMBRANE-TYPE-1 MATRIX METALLOPROTEINASE, MT1MMP

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCHLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4GOL2Ligand/IonGLYCEROL
5MG1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:52 , GLY A:54 , ARG A:56binding site for residue CL A 301
02AC2SOFTWAREGLN A:39 , THR A:40 , PRO A:41 , LYS A:43 , HOH A:432binding site for residue GOL A 302
03AC3SOFTWAREARG A:56 , ARG A:72 , ASP A:73 , ASN A:74 , HOH A:401 , HOH A:402binding site for residue EPE A 303
04AC4SOFTWAREHIS B:31 , SER B:32 , ASN B:33 , ASN C:225 , HOH C:309binding site for residue EDO B 301
05AC5SOFTWARESER H:52 , GLY H:54 , GLY H:55 , ARG H:56binding site for residue CL H 301
06AC6SOFTWAREGLN H:39 , THR H:40 , PRO H:41 , LYS H:43 , HOH H:439binding site for residue GOL H 302
07AC7SOFTWAREARG H:56 , ARG H:72 , ASP H:73 , ASN H:74 , HOH H:447binding site for residue EPE H 303
08AC8SOFTWARELYS H:148 , GLY H:149 , LEU H:179 , THR H:181 , HOH H:479 , HOH H:556binding site for residue EDO H 304
09AC9SOFTWAREHOH H:423 , HOH L:412 , HOH L:419 , HOH L:430 , HOH L:436 , HOH L:448binding site for residue MG L 301
10AD1SOFTWAREASP M:216binding site for residue EDO M 301

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:145 -A:200
3B:23 -B:93
4B:140 -B:200
5H:22 -H:96
6H:145 -H:200
7L:23 -L:93
8L:140 -L:200

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Phe A:151 -Pro A:152
2Glu A:153 -Pro A:154
3Trp A:193 -Pro A:194
4Thr B:7 -Pro B:8
5Ala B:99 -Pro B:100
6Tyr B:146 -Pro B:147
7Phe H:151 -Pro H:152
8Glu H:153 -Pro H:154
9Trp H:193 -Pro H:194
10Thr L:7 -Pro L:8
11Ala L:99 -Pro L:100
12Tyr L:146 -Pro L:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P3D)

(-) Exons   (0, 0)

(no "Exon" information available for 4P3D)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p3d A   1 EVKLVESGGGLVKPGGSLKLSCAASGFIFSNYAMSWVRQTPEKRLEWVATISGGGRNIYSLDSVKGRFTFFRDNARNTLYLQMSSLRSEDTAMYFCSRENYGSSFTYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee........eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeeee........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p3d B   1 DVLMTQTPLSLPVGLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHAPYTFGGGTKLEIKRAADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4p3d C 215 FDSAEPWTVRNED 227
                                   224   


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p3d H   1 EVKLVESGGGLVKPGGSLKLSCAASGFIFSNYAMSWVRQTPEKRLEWVATISGGGRNIYSLDSVKGRFTFFRDNARNTLYLQMSSLRSEDTAMYFCSRENYGSSFTYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee........eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..eee...eeeeee........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p3d L   1 DVLMTQTPLSLPVGLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHAPYTFGGGTKLEIKRAADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        


Chain M from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4p3d M 215 FDSAEPWTVRNED 227
                                   224
   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 4P3D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P3D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P3D)

(-) Gene Ontology  (55, 55)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:99 - Pro B:100   [ RasMol ]  
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    Glu A:153 - Pro A:154   [ RasMol ]  
    Glu H:153 - Pro H:154   [ RasMol ]  
    Phe A:151 - Pro A:152   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Thr B:7 - Pro B:8   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp A:193 - Pro A:194   [ RasMol ]  
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    Tyr L:146 - Pro L:147   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP14_HUMAN | P50281: 1bqq 1buv 2mqs 3c7x 3ma2 3x23 4p3c 4qxu
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2a1w 2dqt 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

4p3c