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(-) Description

Title :  THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION
 
Authors :  J. P. Griffith, S. Song, M. G. Rossmann
Date :  04 Jan 88  (Deposition) - 12 Jul 89  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  1,2,3,4
Keywords :  Oxidoreductase(Aldehyde(D)-Nad(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Murthy, R. M. Garavito, J. E. Johnson, M. G. Rossmann
Structure Of Lobster Apo-D-Glyceraldehyde-3-Phosphate Dehydrogenase At 3. 0 A Resolution.
J. Mol. Biol. V. 138 859 1980
PubMed-ID: 7411626  |  Reference-DOI: 10.1016/0022-2836(80)90069-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
    Chains: 1, 2, 3, 4
    EC Number: 1.2.1.12
    Engineered: YES
    Organism Common: AMERICAN LOBSTER
    Organism Scientific: HOMARUS AMERICANUS
    Organism Taxid: 6706

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : 1234

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4GPD)

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AB1AUTHORASN 1:6 , ASN 1:30 , ASP 1:31 , PHE 1:33 , THR 1:95 , PHE 1:98RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
02AB2AUTHORASN 2:6 , ASN 2:30 , ASP 2:31 , PHE 2:33 , THR 2:95 , PHE 2:98RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
03AB3AUTHORASN 3:6 , ASN 3:30 , ASP 3:31 , PHE 3:33 , THR 3:95 , PHE 3:98RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
04AB4AUTHORASN 4:6 , ASN 4:30 , ASP 4:31 , PHE 4:33 , THR 4:95 , PHE 4:98RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
05AP1AUTHORARG 1:10 , ALA 1:179RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR.
06AP2AUTHORARG 2:10 , ALA 2:179RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR.
07AP3AUTHORARG 3:10 , ALA 3:179RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR.
08AP4AUTHORARG 4:10 , ALA 4:179RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR.
09AR1AUTHORGLY 1:7 , ASP 1:31RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
10AR2AUTHORGLY 2:7 , ASP 2:31RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
11AR3AUTHORGLY 3:7 , ASP 3:31RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
12AR4AUTHORGLY 4:7 , ASP 4:31RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
13NB1UNKNOWNILE 1:11 , CYS 1:148 , ASN 1:312 , TYR 1:316NULL
14NB2UNKNOWNILE 2:11 , CYS 2:148 , ASN 2:312 , TYR 2:316NULL
15NB3UNKNOWNILE 3:11 , CYS 3:148 , ASN 3:312 , TYR 3:316NULL
16NB4UNKNOWNILE 4:11 , CYS 4:148 , ASN 4:312 , TYR 4:316NULL
17NP1AUTHORILE 1:11RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
18NP2AUTHORILE 2:11RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
19NP3AUTHORILE 3:11RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
20NP4AUTHORILE 4:11RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
21NR1AUTHORTHR 1:95 , GLY 1:96 , SER 1:118 , ALA 1:119RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
22NR2AUTHORTHR 2:95 , GLY 2:96 , SER 2:118 , ALA 2:119RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
23NR3AUTHORTHR 3:95 , GLY 3:96 , SER 3:118 , ALA 3:119RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
24NR4AUTHORTHR 4:95 , GLY 4:96 , SER 4:118 , ALA 4:119RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GPD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GPD)

(-) 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 1 from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gpd11 1:1-147,1:312-333 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d4gpd12 1:148-311 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d4gpd11                SCOP domains
               CATH domains 4gpd101 1:1-146,1:313-332 NAD(P)-binding Rossmann-like Domain                                                                                     4gpd102 1:147-312 Dihydrodipicolinate Reductase; domain 2                                                                                                             4gpd101             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........eeeee..eeeee....eee...............eeeeee.....hhhhhhhhhhhh..eeeeee.....eee.............eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeeeeee.........eeeeehhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh.....eee................eeee.....eee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpd 1   1 SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   


Chain 2 from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gpd21 2:1-147,2:312-333 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d4gpd22 2:148-311 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d4gpd21                SCOP domains
               CATH domains 4gpd201 2:1-146,2:313-332 NAD(P)-binding Rossmann-like Domain                                                                                     4gpd202 2:147-312 Dihydrodipicolinate Reductase; domain 2                                                                                                             4gpd201             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........eeeee..eeeee....eee...............eeeeee.....hhhhhhhhhhhh..eeeeee.....eee.............eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeeeeee.........eeeeehhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh.....eee................eeee.....eee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpd 2   1 SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   


Chain 3 from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gpd31 3:1-147,3:312-333 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d4gpd32 3:148-311 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d4gpd31                SCOP domains
               CATH domains 4gpd301 3:1-146,3:313-332 NAD(P)-binding Rossmann-like Domain                                                                                     4gpd302 3:147-312 Dihydrodipicolinate Reductase; domain 2                                                                                                             4gpd301             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........eeeee..eeeee....eee...............eeeeee.....hhhhhhhhhhhh..eeeeee.....eee.............eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeeeeee.........eeeeehhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh.....eee................eeee.....eee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpd 3   1 SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   


Chain 4 from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gpd41 4:1-147,4:312-333 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d4gpd42 4:148-311 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d4gpd41                SCOP domains
               CATH domains 4gpd401 4:1-146,4:313-332 NAD(P)-binding Rossmann-like Domain                                                                                     4gpd402 4:147-312 Dihydrodipicolinate Reductase; domain 2                                                                                                             4gpd401             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........eeeee..eeeee....eee...............eeeeee.....hhhhhhhhhhhh..eeeeee.....eee.............eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeeeeee.........eeeeehhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh.....eee................eeee.....eee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpd 4   1 SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   Legend:   → Mismatch (orange background)
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  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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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