Structure of PDB 4nmc Chain B Binding Site BS01

Receptor Information

>4nmc Chain B (length=969) Species: 243231 (Geobacter sulfurreducens PCA)

NSELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQM
FRFVDVFPSLTTSKLLTEHIREYFGGGAVLNKVLTSNIEEMARQFIVGET
TKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKE
QGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAIL
DRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIV
LQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEV
PVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELN
VPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLL
ENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARAGLGGLPPFNNEA
MVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNK
PSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAAR
KRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGH
APGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGI
TSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGS
METGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVL
YSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYM
GAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPE
HRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKA
RREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPR
VVTENTMRRGFAPIEEDDD

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[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)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[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)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 4nmc Chain B Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4nmc Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
• Resolution: 1.901 Å
• Binding residue (original residue number in PDB): D244 M245 V274 Q276 R303 V305 K306 G307 A308 Y309 W310 W327 T328 I329 K330 S333 A356 S357 H358 N359 L385 E425 S431 F432
• Binding residue (residue number reindexed from 1): D220 M221 V250 Q252 R279 V281 K282 G283 A284 Y285 W286 W303 T304 I305 K306 S309 A332 S333 H334 N335 L361 E401 S407 F408
• 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): N623 K646 E727 C761 E857 A937
• 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:4nmc, PDBe:4nmc, PDBj:4nmc
• PDBsum: 4nmc
• PubMed: 24550478
• UniProt: Q746X3