PDB ID : 3gmd [A2]

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ARa IRb





 a AR:All Residues
 b IR:Interface Residues

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Secondary Structure


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Chain
Chain name Ribbon Spacefill Cαonly
OLIGAMI PDB
AA
BB
Title
STRUCTURE-BASED DESIGN OF 7-AZAINDOLE-PYRROLIDINES AS INHIBITORS OF 11BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE I

Structure Summary
PDB ID Mutant OPM Pub Med Method/Resolution HETNAM
3gmd
22901389 X-RAY DIFFRACTION/2.28 2M3:2-METHYL-3-{(3S)-1-[(1-PYRIDIN-2-YLCYCLOPROPYL)CARBONYL]PYRROLIDIN-3-YL}-1H-PYRROLO[2,3-B]PYRIDINE
NDP:NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
SO4:SULFATE ION
Chain Formula
Amino Acid sequence SCOPe Family Level CATH Homology Level
[A2] [A2] [A2]

Interfaces
Interface ID Chain Inaterface
Class		 Interface Type Contact Type
3gmd_AB A
B		 HN
HN		 i7_CR(H35,N24)_HH(A1,S4)_HN(L3,S9)
i7_CR(H35,N24)_HH(A1,S4)_HN(L3,S9) 		c4_RP(HH52,NN42,HN39,NH36,EN1)_HH(P2,A3,S6)_HN(L8,S9)
c4_RP(HH52,NN42,HN39,NH36,EN1)_HH(P2,A3,S6)_HN(L8,S9)

Interface Class
Interface ID Interface 1 Interface 2
Domain Number of contact residues Binding site Class Percentages of Secondary structures(%) Domain Number of contact residues Binding site Class Percentages of Secondary structures(%)
H E N H E N
3gmd_AB A 57 HN 50.9 100 49.1 B 55 HN 47.3 0 52.7

Interface Type: Information for each interface
Interface ID chain Number of contact residues Number of elements Number of contacts between Secondary structure elements
HH EE HE HN EN
Hn En Nn H E N R L P A S P A S Ph Ah Ih P A S L S L S
3gmd_AB A 29 57 28 6 0 7 0 0 0 0 4 0 0 0 0 0 0 0 0 0 2 11 0 0
3gmd_AB B 26 0 29 5 0 7 0 0 0 0 4 0 0 0 0 0 0 0 0 0 2 10 0 0

Contact Type: Information of contacts between interfaces
Interface ID Number of residue pairs between SS elements Number of contacts between Secondary structure elements
H-H E-E N-N H-E H-N N-E E-H N-H E-N H-H E-E H-E H-N E-N
P A S Ih P A S IPh IAh P A S Ih L S Ih L S Ih
3gmd_AB 38 0 37 0 32 0 0 38 0 0 2 8 0 0 0 0 0 0 0 0 0 0 9 5 0 0 0 0

Structual Classification
SCOPe
SCOPe ID Chain Class Fold Superfamily Family Protein Domain Species
176741 A:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176742 B:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176743 C:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176744 D:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176745 E:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176746 F:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176747 G:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]
176748 H:Alpha and beta proteins (a/b)NAD(P)-binding Rossmann-fold domainsNAD(P)-binding Rossmann-fold domainsTyrosine-dependent oxidoreductases11-beta-hydroxysteroid dehydrogenase 1Mouse (Mus musculus) [TaxId: 10090]

CATH
CATH ID Node Class Architecture Topology Homology
3gmdA003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdB003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdC003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdD003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdE003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdF003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdG003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain
3gmdH003.40.50.720:3-Layer(aba) Sandwich:Rossmann fold:NAD(P)-binding Rossmann-like Domain