2024-08-31_00000087|ligand|8S3D

Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2-amino-2-hydroxyglutarate (reaction intermediate) and NAD; X-ray diffraction 1.65Å
Protein #1 414 residues (100% resolved)

SNAMNALVATNRNFQRASRILGLDSKLEKSLLIPYREIKVECTIPKDDGSLVSYVGFRIQHDNARGPMKGGIRYHPEVDPDEVNALAQLMTWKTAVVDIPYGGAKGGIGCNPKDLSISELERLTRVFTQKIHDLIGIHRDVPAPDMGTNSQTMAWILDEYSKFHGHSPAVVTGKPIDLGGSLGREAATGLGVVFATEALFAEYGKSISDMTFAIQGFGNVGTWAAKAIFERGGKVVAVSDINGAISNPNGIDIAALLKHKAGNGSLKDFSGGDAMNPNDLLVHDCDVLIPCALGGVLNKENANDVKAKFIIEAANHPTDPDADEILSKKGVIILPDVYANAGGVTVSYFEWVQNIQGFMWDEEKVNQELKRYMTKAFNDIKANCKTHNCDLRMGAFTLGLNRVARATLLRGWEA

SNAMNALVATNRNFQRASRILGLDSKLEKSLLIPYREIKVECTIPKDDGSLVSYVGFRIQHDNARGPMKGGIRYHPEVDPDEVNALAQLMTWKTAVVDIPYGGAKGGIGCNPKDLSISELERLTRVFTQKIHDLIGIHRDVPAPDMGTNSQTMAWILDEYSKFHGHSPAVVTGKPIDLGGSLGREAATGLGVVFATEALFAEYGKSISDMTFAIQGFGNVGTWAAKAIFERGGKVVAVSDINGAISNPNGIDIAALLKHKAGNGSLKDFSGGDAMNPNDLLVHDCDVLIPCALGGVLNKENANDVKAKFIIEAANHPTDPDADEILSKKGVIILPDVYANAGGVTVSYFEWVQNIQGFMWDEEKVNQELKRYMTKAFNDIKANCKTHNCDLRMGAFTLGLNRVARATLLRGWEA
Non polymer #2 8GL

InChI=1S/C5H9NO5/c6-5(11,4(9)10)2-1-3(7)8/h11H,1-2,6H2,(H,7,8)(H,9,10)/t5-/m0/s1

C(C[C@](C(=O)O)(N)O)C(=O)O
Non polymer #3 CA

InChI=1S/Ca/q+2

[Ca+2]
Non polymer #4 EDO

InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2

C(CO)O
Non polymer #5 GLY

InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)

C(C(=O)O)N
Non polymer #6 NA

InChI=1S/Na/q+1

[Na+]
Non polymer #7 NAD

InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1

c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
Non polymer #8 PEG

InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2

C(COCCO)O
Non polymer #9 PG4

InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2

C(COCCOCCOCCO)O
Non polymer #10 PGE

InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2

C(COCCOCCO)O
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Reference