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(-) Description

Title :  STRUCTURE OF FRIL, A LEGUME LECTIN THAT DELAYS HEMATOPOIETIC PROGENITOR MATURATION
 
Authors :  T. W. Hamelryck, J. G. Moore, M. Chrispeels, R. Loris, L. Wyns
Date :  04 Oct 99  (Deposition) - 10 Oct 99  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Lectin, Crosslink, Hematopoietic Progenitor, Sugar Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. W. Hamelryck, J. G. Moore, M. J. Chrispeels, R. Loris, L. Wyns
The Role Of Weak Protein-Protein Interactions In Multivalent Lectin-Carbohydrate Binding: Crystal Structure Of Cross-Linked Fril
J. Mol. Biol. V. 299 875 2000
PubMed-ID: 10843844  |  Reference-DOI: 10.1006/JMBI.2000.3785
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE BINDING LECTIN, FRIL
    ChainsA, B, C, D
    FragmentALPHA CHAIN RESIDUES 1 TO 113
    OrganSEED
    Organism CommonFIELD BEAN
    Organism ScientificDOLICHOS LAB LAB
    Organism Taxid35936
 
Molecule 2 - MANNOSE BINDING LECTIN, FRIL
    ChainsE, F, G, H
    FragmentBETA CHAIN RESIDUES 132 TO 264
    OrganSEED
    Organism CommonFIELD BEAN
    Organism ScientificDOLICHOS LAB LAB
    Organism Taxid35936

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MAN4Ligand/IonALPHA-D-MANNOSE
3MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:86 , GLY A:104 , TYR E:142 , ASN E:144 , TYR E:147 , GLY E:228 , GLN E:229 , ASP E:230BINDING SITE FOR RESIDUE MAN A 302
02AC2SOFTWAREASP B:86 , GLY B:104 , TYR F:142 , ASN F:144 , TYR F:147 , GLY F:228 , GLN F:229 , ASP F:230BINDING SITE FOR RESIDUE MAN B 302
03AC3SOFTWAREASP C:86 , GLY C:104 , TYR G:142 , ASN G:144 , TYR G:147 , GLY G:228 , GLN G:229 , ASP G:230BINDING SITE FOR RESIDUE MAN C 302
04AC4SOFTWAREASP D:86 , GLY D:104 , TYR H:142 , ASN H:144 , TYR H:147 , GLY H:228 , GLN H:229 , ASP H:230BINDING SITE FOR RESIDUE MAN D 302
05AC5SOFTWAREASP E:140 , TYR E:142 , ASN E:144 , ASP E:149BINDING SITE FOR RESIDUE CA A 300
06AC6SOFTWAREGLU E:138 , ASP E:140 , ASP E:149 , HIS E:154BINDING SITE FOR RESIDUE MN A 301
07AC7SOFTWAREASP F:140 , TYR F:142 , ASN F:144 , ASP F:149BINDING SITE FOR RESIDUE CA B 300
08AC8SOFTWAREGLU F:138 , ASP F:140 , ASP F:149 , HIS F:154BINDING SITE FOR RESIDUE MN B 301
09AC9SOFTWAREASP G:140 , TYR G:142 , ASN G:144 , ASP G:149BINDING SITE FOR RESIDUE CA C 300
10BC1SOFTWAREGLU G:138 , ASP G:140 , ASP G:149 , HIS G:154BINDING SITE FOR RESIDUE MN C 301
11BC2SOFTWAREASP H:140 , TYR H:142 , ASN H:144 , ASP H:149BINDING SITE FOR RESIDUE CA D 300
12BC3SOFTWAREGLU H:138 , ASP H:140 , ASP H:149 , HIS H:154BINDING SITE FOR RESIDUE MN D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QMO)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:85 -Asp A:86
2Ala B:85 -Asp B:86
3Ala C:85 -Asp C:86
4Ala D:85 -Asp D:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QMO)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.FRIL_LABPU143-149
 
 
 
  4E:135-141
F:135-141
G:135-141
H:135-141
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.FRIL_LABPU223-232
 
 
 
  4E:215-224
F:215-224
G:215-224
H:215-224

(-) Exons   (0, 0)

(no "Exon" information available for 1QMO)

(-) 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:113
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:113
                                    18        28        38        48        58        68        78        88        98       108       118   
           FRIL_LABPU     9 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 121
               SCOP domains d1qmo.1 A:,E: Legume lectin                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee........................eeeeee..........eeeeeeeeeeeeeee.........eeeeeee........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo A   1 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 113
                                    10        20        30        40        50        60        70        80        90       100       110   

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:113
                                    18        28        38        48        58        68        78        88        98       108       118   
           FRIL_LABPU     9 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 121
               SCOP domains d1qmo.2 B:,F: Legume lectin                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee........................eeeeee..........eeeeeeeeeeeeeee.........eeeeeee........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo B   1 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 113
                                    10        20        30        40        50        60        70        80        90       100       110   

Chain C from PDB  Type:PROTEIN  Length:113
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:113
                                    18        28        38        48        58        68        78        88        98       108       118   
           FRIL_LABPU     9 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 121
               SCOP domains d1qmo.3 C:,G: Legume lectin                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee........................eeeeee..........eeeeeeeeeeeeeee.........eeeeeee........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo C   1 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 113
                                    10        20        30        40        50        60        70        80        90       100       110   

Chain D from PDB  Type:PROTEIN  Length:113
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:113
                                    18        28        38        48        58        68        78        88        98       108       118   
           FRIL_LABPU     9 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 121
               SCOP domains d1qmo.4 D:,H: Legume lectin                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee........................eeeeee..........eeeeeeeeeeeeeee.........eeeeeee........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo D   1 AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNAN 113
                                    10        20        30        40        50        60        70        80        90       100       110   

Chain E from PDB  Type:PROTEIN  Length:117
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:117
                                   149       159       169       179       189       199       209       219       229       239       249       
           FRIL_LABPU   140 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 256
               SCOP domains d1qmo.1 A:,E: Legume lectin                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee......eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo E 132 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 248
                                   141       151       161       171       181       191       201       211       221       231       241       

Chain F from PDB  Type:PROTEIN  Length:117
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:117
                                   149       159       169       179       189       199       209       219       229       239       249       
           FRIL_LABPU   140 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 256
               SCOP domains d1qmo.2 B:,F: Legume lectin                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee......eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo F 132 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 248
                                   141       151       161       171       181       191       201       211       221       231       241       

Chain G from PDB  Type:PROTEIN  Length:117
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:117
                                   149       159       169       179       189       199       209       219       229       239       249       
           FRIL_LABPU   140 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 256
               SCOP domains d1qmo.3 C:,G: Legume lectin                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee......eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo G 132 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 248
                                   141       151       161       171       181       191       201       211       221       231       241       

Chain H from PDB  Type:PROTEIN  Length:117
 aligned with FRIL_LABPU | Q9ZTA9 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:117
                                   149       159       169       179       189       199       209       219       229       239       249       
           FRIL_LABPU   140 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 256
               SCOP domains d1qmo.4 D:,H: Legume lectin                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhh.....eeeeee......eeee........eeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee......eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1qmo H 132 SNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTSYYAGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN 248
                                   141       151       161       171       181       191       201       211       221       231       241       

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1QMO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QMO)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (FRIL_LABPU | Q9ZTA9)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
cellular component
    GO:0034495    protein storage vacuole lumen    The volume enclosed by the protein storage vacuole membrane.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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