Structure of PDB 4x9m Chain A Binding Site BS01

Receptor Information

>4x9m Chain A (length=384) Species: 272634 (Mycoplasmoides pneumoniae M129) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

METRDVLIVGGGVIGCATAYELSQYKLKVTLVEKHHYLAQETSHANSGVI
HTGIDPNPHKLTAKYNILGKKLWLNTYFKRLGFPRQKIRTLIVAFNEMER
EQLEVLKQRGIANQINLEDIQMLSKEETLKLEPYVNPEIVAGLKIEGSWA
IDPVLASKCLALAAQQNKVQICTNTEVTNISKQVDGTYLVWTNNETTPSF
KVKKIIDAAGHYADYLAHLAKADDFEQTTRRGQYVVVTNQGELHLNSMVF
MVPTIHGKGVIVSPMLDGNFLVGPTALDGVDKEATRYITKDAPCMLTKIG
KHMVPSLNINNALISFAGSRPIDKATNDFIIRVAHNDPDFVILGGMKSPG
LTAAPAIVREAVRLLNWKLTKKPNWNGKYNLPWI

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

Software	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

PDB chain

4x9m Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	4x9m Structure and proposed mechanism of l-alpha-glycerophosphate oxidase from Mycoplasma pneumoniae.
Resolution	2.4 Å
Binding residue (original residue number in PDB)	G10 G12 I14 E33 K34 E41 T42 S43 A45 N46 S47 V49 H51 E176 V177 A209 G210 Y212 Y234 S319 R320 M346 K347 S348 P349 G350 L351 T352
Binding residue (residue number reindexed from 1)	G10 G12 I14 E33 K34 E41 T42 S43 A45 N46 S47 V49 H51 E176 V177 A209 G210 Y212 Y234 S319 R320 M346 K347 S348 P349 G350 L351 T352
Annotation score	1

Enzymatic activity

Enzyme Commision number

1.1.3.21: glycerol-3-phosphate oxidase.

External links

PDB	RCSB:4x9m, PDBe:4x9m, PDBj:4x9m
PDBsum	4x9m
PubMed	25688572
UniProt	P75063\|GLPO_MYCPN Glycerol 3-phosphate oxidase (Gene Name=glpD)

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