Structure of PDB 4nmf Chain B Binding Site BS01

Receptor Information

>4nmf Chain B (length=979) Species: 243231 (Geobacter sulfurreducens PCA)

ELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFR
FVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQF
IVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLE
ALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGS
VVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYP
HLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQ
NDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEM
ARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYL
VRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARAARKGLGG
LPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDL
IPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYL
LKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRL
GQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNC
VVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDI
SLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADL
DEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGP
SEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMT
IIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSR
SPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDY
LLHFMDPRVVTENTMRRGFAPIEEDDDWV

Ligand information

• Ligand ID: P5F
• InChI: InChI=1S/C32H40N10O17P2/c1-14-6-16-17(7-15(14)2)41(29-23(30(50)39-32(51)38-29)40(16)5-3-4-34-8-21(45)46)9-18(43)24(47)19(44)10-56-60(52,53)59-61(54,55)57-11-20-25(48)26(49)31(58-20)42-13-37-22-27(33)35-12-36-28(22)42/h3-7,12-13,18-20,24-26,31,43-44,47-49H,8-11H2,1-2H3,(H,45,46)(H,52,53)(H,54,55)(H2,33,35,36)(H2,38,39,50,51)/b5-3+,34-4?/t18-,19+,20+,24-,25+,26+,31+/m0/s1
• InChIKey: IRSTVKNHNHEQIM-RDJFLKOLSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC1=CC2=[N](C3=C(C(=O)NC(=O)N3)[N](=C2C=C1C)C=CC=NCC(=O)O)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.7.6: CC1=CC2=[N](C3=C(C(=O)NC(=O)N3)[N](=C2C=C1C)C=CC=NCC(=O)O)C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.385: Cc1cc2c(cc1C)n(C=CC=NCC(O)=O)c3C(=O)NC(=O)Nc3n2C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56
  CACTVS 3.385: Cc1cc2c(cc1C)n(\C=C\C=NCC(O)=O)c3C(=O)NC(=O)Nc3n2C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56
• Formula: C32 H40 N10 O17 P2
• Name: N-propargylglycine-modified flavin adenine dinucleotide
• PDB chain: 4nmf Chain B Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4nmf Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): K203 D244 M245 V274 Q276 R303 V305 K306 G307 A308 W310 W327 T328 I329 K330 S333 A356 S357 H358 N359 Q383 L385 Y406 E425 E430 S431 F432
• Binding residue (residue number reindexed from 1): K184 D225 M226 V255 Q257 R284 V286 K287 G288 A289 W291 W308 T309 I310 K311 S314 A337 S338 H339 N340 Q364 L366 Y387 E406 E411 S412 F413
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): N655 K678 E759 C793 E889 A969
• Catalytic site (residue number reindexed from 1): N631 K654 E735 C769 E865 A945
• Enzyme Commision number: 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003700 DNA-binding transcription factor activity
• GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
• GO:0004657 proline dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0006562 proline catabolic process
• GO:0010133 proline catabolic process to glutamate

Cellular Component

• GO:0005737 cytoplasm
• GO:0009898 cytoplasmic side of plasma membrane

External links

• PDB: RCSB:4nmf, PDBe:4nmf, PDBj:4nmf
• PDBsum: 4nmf
• PubMed: 24550478
• UniProt: Q746X3