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(-) Description

Title :  MT1-MMP:FAB COMPLEX (FORM I)
 
Authors :  H. Rozenberg, Y. Udi, I. Sagi
Date :  06 Mar 14  (Deposition) - 17 Dec 14  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  H,L,M
Biol. Unit 1:  H,L,M  (2x)
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: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MT1-MMP V-B LOOP
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - LIGHT CHAIN FAB FRAGMENT OF ANTIBODY LEM-2/15
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - MATRIX METALLOPROTEINASE-14
    Chains: 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
    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

  123
Asymmetric Unit : HLM
Biological Unit 1 (2x): HLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO12Ligand/Ion1,2-ETHANEDIOL
4EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER H:52 , GLY H:54 , GLY H:55 , ARG H:56 , HOH L:425binding site for residue CL H 301
02AC2SOFTWAREARG H:56 , ARG H:72 , ASP H:73 , ASN H:74 , HOH H:441 , HOH H:446 , THR L:7 , PRO L:8 , SER L:133 , GLY L:134binding site for residue EPE H 302
03AC3SOFTWARESER H:25 , ASN H:77 , ASN H:138 , SER H:139 , MET H:140 , HOH H:434binding site for residue EDO H 303
04AC4SOFTWAREPRO H:131 , GLY H:132 , SER H:133 , ALA H:134 , HOH H:542 , HOH H:564 , SER L:122 , ILE L:123 , PHE L:124 , HOH L:593 , HOH L:594binding site for residue EDO H 304
05AC5SOFTWAREGLN H:39 , THR H:40 , PRO H:41 , LYS H:43 , HOH H:472binding site for residue EDO H 305
06AC6SOFTWAREGLU H:153 , PRO H:154 , VAL H:155 , ALA H:173 , LEU H:182binding site for residue EDO H 306
07AC7SOFTWARETYR H:59 , HOH H:405 , SER L:97 , ALA L:99 , HOH L:410 , HOH L:490 , HOH L:510 , HOH L:521binding site for residue EDO H 307
08AC8SOFTWAREPHE H:171 , PRO H:172 , VAL H:174 , THR H:181 , LEU H:182 , SER H:183 , HOH H:474 , SER L:168 , SER L:182binding site for residue ACT H 308
09AC9SOFTWAREASN H:100 , TYR H:101 , SER H:103 , HOH H:521 , HOH H:571 , TYR L:54 , PHE L:60binding site for residue ACT H 309
10AD1SOFTWAREHOH H:415 , ASP L:17 , HOH L:428 , HOH L:438 , HOH L:455 , HOH L:485binding site for residue MG L 301
11AD2SOFTWAREHIS L:31 , SER L:32 , ASN L:33 , ASN M:225 , HOH M:311binding site for residue EDO L 302
12AD3SOFTWARELYS L:44 , GLU L:86 , ASP L:87 , HOH L:591binding site for residue ACT L 303

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:145 -H:200
3L:23 -L:93
4L:140 -L:200

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Pro H:131 -Gly H:132
2Phe H:151 -Pro H:152
3Glu H:153 -Pro H:154
4Trp H:193 -Pro H:194
5Thr L:7 -Pro L:8
6Ala L:99 -Pro L:100
7Tyr L:146 -Pro L:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P3C)

(-) Exons   (0, 0)

(no "Exon" information available for 4P3C)

(-) 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 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
                 4p3c 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..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeeee........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p3c 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
                 4p3c 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 4P3C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P3C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P3C)

(-) Gene Ontology  (55, 55)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala L:99 - Pro L:100   [ RasMol ]  
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    Thr L:7 - Pro L:8   [ RasMol ]  
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    Tyr L:146 - Pro L:147   [ RasMol ]  
 
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        MMP14_HUMAN | P50281: 1bqq 1buv 2mqs 3c7x 3ma2 3x23 4p3d 4qxu

(-) Related Entries Specified in the PDB File

4ouu FREE FAB LEM 2/15
4p3d