PDB entry 6p87

View 6p87 on RCSB PDB site
Description: e.coli lpxd in complex with compound 5
Deposited on 2019-06-06, released 2019-08-28
The last revision was dated 2020-06-24, with a file datestamp of 2020-06-19.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: N/A
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
    Species: Escherichia coli [TaxId:562]
    Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, AUS26_23195, AW059_09890, AW106_08805, B1K96_12940, B7C53_01310, BANRA_00558, BANRA_00653, BANRA_02262, BANRA_03350, BET08_19125, BHF46_07835, BHS81_00700, BHS87_00855, BIZ41_19025, BJJ90_21310, BK292_13720, BK400_03560, BMT53_09465, BN17_46021, BTQ06_06540, BUE81_01655, BVL39_02135, BW690_02415, BZL31_14885, C2U48_09555, C4J69_03380, C5N07_08630, C5P01_08975, C5P43_07335, C6669_04195, C6986_01145, C7235_20180, C7B06_05915, C7B07_04225, CA593_02815, CG691_14440, CG692_09445, CG705_12975, CG706_12690, COD30_14715, COD46_06685, CR538_20590, CR539_04985, CRM83_15040, CXB56_23080, D0X26_09365, D2184_08545, D2185_20180, D2F89_01460, D3821_06260, D3O91_03240, D3Y67_16455, D9D20_18680, D9D55_03030, D9D69_06830, D9E22_13300, D9E35_14480, D9G42_07535, D9H66_18155, D9H68_13825, D9I18_15010, D9I87_01590, D9I97_03755, D9J11_16875, D9J44_14030, DIV22_06320, DL545_20340, DMZ31_06810, DNQ41_04690, DNQ45_10065, DQF57_05615, DQO13_06200, DS732_05825, DTL43_05870, EAI42_08350, EAI46_03595, EAI52_11055, EC1094V2_3672, EC3234A_2c01610, EC3426_00931, EC382_03005, ECTO6_03883, ED287_04550, ED600_04595, EEP23_00115, EFV01_09910, EFV02_20465, EFV04_15215, EFV08_17150, EFV11_08135, EFV12_18845, EFV15_17225, EFV17_09875, EIA13_13600, EL75_3585, EL79_3695, EL80_3642, ERS085374_03841, ERS150873_01122, ERS150876_00054, FORC28_5013, HW43_04650, JD73_13090, NCTC10429_04183, NCTC10865_05054, NCTC11022_04906, NCTC11126_03647, NCTC13462_02218, NCTC8500_04533, NCTC8960_01551, NCTC9037_04178, NCTC9045_04699, NCTC9055_00956, NCTC9058_02808, NCTC9062_04225, NCTC9706_01326, NCTC9969_04255, PU06_22990, RG28_03860, RK56_027945, RX35_04913, SAMEA3472043_02537, SAMEA3472044_04146, SAMEA3472047_02509, SAMEA3472070_02384, SAMEA3472080_03763, SAMEA3472114_03609, SAMEA3484427_01386, SAMEA3484429_01095, SAMEA3752553_02884, SAMEA3752557_00885, SAMEA3752559_03701, SAMEA3753064_03381, SAMEA3753097_03916, SAMEA3753290_00404, SAMEA3753300_01852, SK85_00179, WQ89_09605, WR15_02380
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
    Species: Escherichia coli [TaxId:562]
    Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, AUS26_23195, AW059_09890, AW106_08805, B1K96_12940, B7C53_01310, BANRA_00558, BANRA_00653, BANRA_02262, BANRA_03350, BET08_19125, BHF46_07835, BHS81_00700, BHS87_00855, BIZ41_19025, BJJ90_21310, BK292_13720, BK400_03560, BMT53_09465, BN17_46021, BTQ06_06540, BUE81_01655, BVL39_02135, BW690_02415, BZL31_14885, C2U48_09555, C4J69_03380, C5N07_08630, C5P01_08975, C5P43_07335, C6669_04195, C6986_01145, C7235_20180, C7B06_05915, C7B07_04225, CA593_02815, CG691_14440, CG692_09445, CG705_12975, CG706_12690, COD30_14715, COD46_06685, CR538_20590, CR539_04985, CRM83_15040, CXB56_23080, D0X26_09365, D2184_08545, D2185_20180, D2F89_01460, D3821_06260, D3O91_03240, D3Y67_16455, D9D20_18680, D9D55_03030, D9D69_06830, D9E22_13300, D9E35_14480, D9G42_07535, D9H66_18155, D9H68_13825, D9I18_15010, D9I87_01590, D9I97_03755, D9J11_16875, D9J44_14030, DIV22_06320, DL545_20340, DMZ31_06810, DNQ41_04690, DNQ45_10065, DQF57_05615, DQO13_06200, DS732_05825, DTL43_05870, EAI42_08350, EAI46_03595, EAI52_11055, EC1094V2_3672, EC3234A_2c01610, EC3426_00931, EC382_03005, ECTO6_03883, ED287_04550, ED600_04595, EEP23_00115, EFV01_09910, EFV02_20465, EFV04_15215, EFV08_17150, EFV11_08135, EFV12_18845, EFV15_17225, EFV17_09875, EIA13_13600, EL75_3585, EL79_3695, EL80_3642, ERS085374_03841, ERS150873_01122, ERS150876_00054, FORC28_5013, HW43_04650, JD73_13090, NCTC10429_04183, NCTC10865_05054, NCTC11022_04906, NCTC11126_03647, NCTC13462_02218, NCTC8500_04533, NCTC8960_01551, NCTC9037_04178, NCTC9045_04699, NCTC9055_00956, NCTC9058_02808, NCTC9062_04225, NCTC9706_01326, NCTC9969_04255, PU06_22990, RG28_03860, RK56_027945, RX35_04913, SAMEA3472043_02537, SAMEA3472044_04146, SAMEA3472047_02509, SAMEA3472070_02384, SAMEA3472080_03763, SAMEA3472114_03609, SAMEA3484427_01386, SAMEA3484429_01095, SAMEA3752553_02884, SAMEA3752557_00885, SAMEA3752559_03701, SAMEA3753064_03381, SAMEA3753097_03916, SAMEA3753290_00404, SAMEA3753300_01852, SK85_00179, WQ89_09605, WR15_02380
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q0P6M7 (4-End)
      • expression tag (3)
  • Chain 'C':
    Compound: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
    Species: Escherichia coli [TaxId:562]
    Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, AUS26_23195, AW059_09890, AW106_08805, B1K96_12940, B7C53_01310, BANRA_00558, BANRA_00653, BANRA_02262, BANRA_03350, BET08_19125, BHF46_07835, BHS81_00700, BHS87_00855, BIZ41_19025, BJJ90_21310, BK292_13720, BK400_03560, BMT53_09465, BN17_46021, BTQ06_06540, BUE81_01655, BVL39_02135, BW690_02415, BZL31_14885, C2U48_09555, C4J69_03380, C5N07_08630, C5P01_08975, C5P43_07335, C6669_04195, C6986_01145, C7235_20180, C7B06_05915, C7B07_04225, CA593_02815, CG691_14440, CG692_09445, CG705_12975, CG706_12690, COD30_14715, COD46_06685, CR538_20590, CR539_04985, CRM83_15040, CXB56_23080, D0X26_09365, D2184_08545, D2185_20180, D2F89_01460, D3821_06260, D3O91_03240, D3Y67_16455, D9D20_18680, D9D55_03030, D9D69_06830, D9E22_13300, D9E35_14480, D9G42_07535, D9H66_18155, D9H68_13825, D9I18_15010, D9I87_01590, D9I97_03755, D9J11_16875, D9J44_14030, DIV22_06320, DL545_20340, DMZ31_06810, DNQ41_04690, DNQ45_10065, DQF57_05615, DQO13_06200, DS732_05825, DTL43_05870, EAI42_08350, EAI46_03595, EAI52_11055, EC1094V2_3672, EC3234A_2c01610, EC3426_00931, EC382_03005, ECTO6_03883, ED287_04550, ED600_04595, EEP23_00115, EFV01_09910, EFV02_20465, EFV04_15215, EFV08_17150, EFV11_08135, EFV12_18845, EFV15_17225, EFV17_09875, EIA13_13600, EL75_3585, EL79_3695, EL80_3642, ERS085374_03841, ERS150873_01122, ERS150876_00054, FORC28_5013, HW43_04650, JD73_13090, NCTC10429_04183, NCTC10865_05054, NCTC11022_04906, NCTC11126_03647, NCTC13462_02218, NCTC8500_04533, NCTC8960_01551, NCTC9037_04178, NCTC9045_04699, NCTC9055_00956, NCTC9058_02808, NCTC9062_04225, NCTC9706_01326, NCTC9969_04255, PU06_22990, RG28_03860, RK56_027945, RX35_04913, SAMEA3472043_02537, SAMEA3472044_04146, SAMEA3472047_02509, SAMEA3472070_02384, SAMEA3472080_03763, SAMEA3472114_03609, SAMEA3484427_01386, SAMEA3484429_01095, SAMEA3752553_02884, SAMEA3752557_00885, SAMEA3752559_03701, SAMEA3753064_03381, SAMEA3753097_03916, SAMEA3753290_00404, SAMEA3753300_01852, SK85_00179, WQ89_09605, WR15_02380
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q0P6M7 (4-End)
      • expression tag (3)
  • Heterogens: O4P, O3V, MG, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6p87A (A:)
gsggsirladlaqqldaelhgdgdivitgvasmqsaqtghitfmvnpkyrehlglcqasa
vvmtqddlpfaksaalvvknpyltyarmaqildttpqpaqniapsavidataklgnnvsi
ganaviesgvelgdnviigagcfvgknskigagsrlwanvtiyheiqigqncliqsgtvv
gadgfgyandrgnwvkipqigrviigdrveigacttidrgalddtiigngviidnqcqia
hnvvigdntavaggvimagslkigrycmiggasvinghmeicdkvtvtgmgmvmrpitep
gvyssgiplqpnkvwrktaalvmniddmskrlkslerkvnqqd

    Sequence, based on observed residues (ATOM records):
    >6p87A (A:)
sirladlaqqldaelhgdgdivitgvasmqsaqtghitfmvnpkyrehlglcqasavvmt
qddlpfaksaalvvknpyltyarmaqildttpqpaqniapsavidataklgnnvsigana
viesgvelgdnviigagcfvgknskigagsrlwanvtiyheiqigqncliqsgtvvgadg
fgyandrgnwvkipqigrviigdrveigacttidrgalddtiigngviidnqcqiahnvv
igdntavaggvimagslkigrycmiggasvinghmeicdkvtvtgmgmvmrpitepgvys
sgiplqpnkvwrktaalvmniddmskrlkslerkv

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6p87B (B:)
gsggsirladlaqqldaelhgdgdivitgvasmqsaqtghitfmvnpkyrehlglcqasa
vvmtqddlpfaksaalvvknpyltyarmaqildttpqpaqniapsavidataklgnnvsi
ganaviesgvelgdnviigagcfvgknskigagsrlwanvtiyheiqigqncliqsgtvv
gadgfgyandrgnwvkipqigrviigdrveigacttidrgalddtiigngviidnqcqia
hnvvigdntavaggvimagslkigrycmiggasvinghmeicdkvtvtgmgmvmrpitep
gvyssgiplqpnkvwrktaalvmniddmskrlkslerkvnqqd

    Sequence, based on observed residues (ATOM records):
    >6p87B (B:)
gsirladlaqqldaelhgdgdivitgvasmqsaqtghitfmvnpkyrehlglcqasavvm
tqddlpfaksaalvvknpyltyarmaqildttpqpaqniapsavidataklgnnvsigan
aviesgvelgdnviigagcfvgknskigagsrlwanvtiyheiqigqncliqsgtvvgad
gfgyandrgnwvkipqigrviigdrveigacttidrgalddtiigngviidnqcqiahnv
vigdntavaggvimagslkigrycmiggasvinghmeicdkvtvtgmgmvmrpitepgvy
ssgiplqpnkvwrktaalvmniddmskrlkslerkvnqq

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6p87C (C:)
gsggsirladlaqqldaelhgdgdivitgvasmqsaqtghitfmvnpkyrehlglcqasa
vvmtqddlpfaksaalvvknpyltyarmaqildttpqpaqniapsavidataklgnnvsi
ganaviesgvelgdnviigagcfvgknskigagsrlwanvtiyheiqigqncliqsgtvv
gadgfgyandrgnwvkipqigrviigdrveigacttidrgalddtiigngviidnqcqia
hnvvigdntavaggvimagslkigrycmiggasvinghmeicdkvtvtgmgmvmrpitep
gvyssgiplqpnkvwrktaalvmniddmskrlkslerkvnqqd

    Sequence, based on observed residues (ATOM records):
    >6p87C (C:)
gsirladlaqqldaelhgdgdivitgvasmqsaqtghitfmvnpkyrehlglcqasavvm
tqddlpfaksaalvvknpyltyarmaqildttpqpaqniapsavidataklgnnvsigan
aviesgvelgdnviigagcfvgknskigagsrlwanvtiyheiqigqncliqsgtvvgad
gfgyandrgnwvkipqigrviigdrveigacttidrgalddtiigngviidnqcqiahnv
vigdntavaggvimagslkigrycmiggasvinghmeicdkvtvtgmgmvmrpitepgvy
ssgiplqpnkvwrktaalvmniddmskrlkslerkvn