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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GASTRIC LIPASE
 
Authors :  A. Roussel, S. Canaan, R. Verger, C. Cambillau
Date :  12 Mar 99  (Deposition) - 15 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Roussel, S. Canaan, M. P. Egloff, M. Riviere, L. Dupuis, R. Verger, C. Cambillau
Crystal Structure Of Human Gastric Lipase And Model Of Lysosomal Acid Lipase, Two Lipolytic Enzymes Of Medical Interest.
J. Biol. Chem. V. 274 16995 1999
PubMed-ID: 10358049  |  Reference-DOI: 10.1074/JBC.274.24.16995

(-) Compounds

Molecule 1 - LIPASE, GASTRIC
    CellCHIEF CELL
    ChainsA, B
    EC Number3.1.1.3
    EngineeredYES
    Expression SystemINSECT CELL
    Expression System VectorBACULOVIRUS
    Expression System Vector TypeVIRUS
    OrganSTOMAC
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:15 , SER A:17 , GLN A:18 , GLU A:29 , TRP A:104 , HOH A:386 , HOH A:387 , HOH A:388BINDING SITE FOR RESIDUE NAG A 1
02AC2SOFTWAREASN A:80 , HOH A:380 , HOH A:381 , HOH A:403BINDING SITE FOR RESIDUE NAG A 2
03AC3SOFTWARENAG A:4 , LEU A:78 , ASN A:252 , ARG A:255BINDING SITE FOR RESIDUE NAG A 3
04AC4SOFTWARENAG A:3BINDING SITE FOR RESIDUE NAG A 4
05AC5SOFTWAREASN A:308 , THR A:310 , HOH A:392BINDING SITE FOR RESIDUE NAG A 5
06AC6SOFTWAREASN B:15 , SER B:17 , GLN B:18 , GLU B:29 , TRP B:104 , HOH B:388 , HOH B:389 , HOH B:390BINDING SITE FOR RESIDUE NAG B 1
07AC7SOFTWARENAG B:3 , ASN B:80 , GLN B:364 , HOH B:382 , HOH B:383 , HOH B:405BINDING SITE FOR RESIDUE NAG B 2
08AC8SOFTWARENAG B:2 , NAG B:4 , LEU B:78 , ASN B:252 , SER B:254 , ARG B:255BINDING SITE FOR RESIDUE NAG B 3
09AC9SOFTWARENAG B:3 , TRP B:23BINDING SITE FOR RESIDUE NAG B 4
10BC1SOFTWAREASN B:308 , THR B:310 , HOH B:393 , HOH B:394BINDING SITE FOR RESIDUE NAG B 5
11SAAUTHORSER A:153 , ASP A:324 , HIS A:353ACTIVE SITE CHAIN A
12SBAUTHORSER B:153 , ASP B:324 , HIS B:353ACTIVE SITE CHAIN B

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:227 -A:236
2B:227 -B:236

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:263 -Pro A:264
2Asn B:263 -Pro B:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011947T161ALIPG_HUMANPolymorphism814628A/BT142A
2UniProtVAR_020565F224ILIPG_HUMANPolymorphism6586145A/BF205I
3UniProtVAR_020566P348TLIPG_HUMANPolymorphism17333991A/BP329T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIPG_HUMAN166-175
 
  2A:147-156
B:147-156

(-) Exons   (9, 18)

Asymmetric/Biological Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002389831aENSE00001157672chr10:90424214-9042424835LIPG_HUMAN-00--
1.3ENST000002389833ENSE00001780304chr10:90427044-90427159116LIPG_HUMAN1-35352A:9-16
B:9-16
8
8
1.4ENST000002389834ENSE00000810580chr10:90427326-90427443118LIPG_HUMAN36-75402A:17-53
B:17-53
37
37
1.5aENST000002389835aENSE00000810581chr10:90428315-90428513199LIPG_HUMAN75-141672A:57-122
B:57-122
66
66
1.6ENST000002389836ENSE00000932776chr10:90429594-90429703110LIPG_HUMAN141-178382A:122-159
B:122-159
38
38
1.7ENST000002389837ENSE00000810583chr10:90431586-90431722137LIPG_HUMAN178-223462A:159-204
B:159-204
46
46
1.8ENST000002389838ENSE00000932779chr10:90433345-90433491147LIPG_HUMAN224-272492A:205-253
B:205-253
49
49
1.9bENST000002389839bENSE00001798606chr10:90435343-9043541472LIPG_HUMAN273-296242A:254-277
B:254-277
24
24
1.10ENST0000023898310ENSE00000810586chr10:90435966-9043603772LIPG_HUMAN297-320242A:278-301
B:278-301
24
24
1.11bENST0000023898311bENSE00000810587chr10:90438202-90438571370LIPG_HUMAN321-398782A:302-379
B:302-379
78
78

(-) 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:368
 aligned with LIPG_HUMAN | P07098 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:371
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397 
           LIPG_HUMAN    28 SPEVTMNISQMITYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK 398
               SCOP domains d1hlga_ A: Gastric lipase                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1hlgA00 A:9-379  [code=3.40.50.1820, no name    defined]                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeee.....eeeeeee........---...eeeee.....hhhhhhh.....hhhhhhhhh..eeee...................hhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee..........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhh........hhhhhhhhhh.......hhhhh...eeeeee......hhhhhhhhhhhh..eeeeeee.....hhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------A--------------------------------------------------------------I---------------------------------------------------------------------------------------------------------------------------T-------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3Exon 1.4  PDB: A:17-53 UniProt: 36-75   -----------------------------------------------------------------Exon 1.6  PDB: A:122-159              ---------------------------------------------Exon 1.8  PDB: A:205-253 UniProt: 224-272        Exon 1.9b  PDB: A:254-27Exon 1.10  PDB: A:278-30Exon 1.11b  PDB: A:302-379 UniProt: 321-398                                    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5a  PDB: A:57-122 UniProt: 75-141 [INCOMPLETE]              ------------------------------------Exon 1.7  PDB: A:159-204 UniProt: 178-223     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1hlg A   9 SPEVTMNISQMITYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSG---QRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK 379
                                    18        28        38        48    |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378 
                                                                       53  57                                                                                                                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:368
 aligned with LIPG_HUMAN | P07098 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:371
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397 
           LIPG_HUMAN    28 SPEVTMNISQMITYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK 398
               SCOP domains d1hlgb_ B: Gastric lipase                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1hlgB00 B:9-379  [code=3.40.50.1820, no name    defined]                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeee....eeeeeeee........---...eeeee.....hhhhhhh.....hhhhhhhhh..eeee..........ee.......hhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh.hhhhhh.eeeeeee..........hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhh........hhhhhhhhhh.......hhhhh...eeeeee......hhhhhhhhhhhh..eeeeeee.....hhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------A--------------------------------------------------------------I---------------------------------------------------------------------------------------------------------------------------T-------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3Exon 1.4  PDB: B:17-53 UniProt: 36-75   -----------------------------------------------------------------Exon 1.6  PDB: B:122-159              ---------------------------------------------Exon 1.8  PDB: B:205-253 UniProt: 224-272        Exon 1.9b  PDB: B:254-27Exon 1.10  PDB: B:278-30Exon 1.11b  PDB: B:302-379 UniProt: 321-398                                    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5a  PDB: B:57-122 UniProt: 75-141 [INCOMPLETE]              ------------------------------------Exon 1.7  PDB: B:159-204 UniProt: 178-223     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1hlg B   9 SPEVTMNISQMITYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSG---QRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK 379
                                    18        28        38        48    |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378 
                                                                       53  57                                                                                                                                                                                                                                                                                                                                  

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LIPG_HUMAN | P07098)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0016615    malate dehydrogenase activity    Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
    GO:0004806    triglyceride lipase activity    Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006108    malate metabolic process    The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006641    triglyceride metabolic process    The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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