SMTL ID : 5ebz.2 (1 other biounit)

Crystal structure of human IKK1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.50 Å

Oligo State

homo-hexamer

Ligands

12 x 5LS- GLC- PDX: 2,3-di-O-sulfo-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-2,4-di-O-sulfo-alpha-D-glucopyranose

5LS-GLC-PDX.1: 7 residues within 4Å: Chain A: S.94, G.96, K.100, K.104, P.105, E.106 Ligands: 5TL.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.106, A:K.104 5LS-GLC-PDX.2: 6 residues within 4Å: Chain A: L.555, R.558, H.587, Q.590, S.591, R.594 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.558, A:R.558 Salt bridges: A:R.594, A:R.594 5LS-GLC-PDX.4: 4 residues within 4Å: Chain B: R.558, K.583, H.587, Q.590 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.558, B:R.558, B:Q.590 5LS-GLC-PDX.5: 7 residues within 4Å: Chain B: K.410 Chain D: K.100, K.104, P.105, E.106, K.564, H.568 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Salt bridges: D:K.564, D:H.568, B:K.410 Hydrogen bonds: D:K.100, D:K.104, D:E.106 5LS-GLC-PDX.6: 4 residues within 4Å: Chain B: K.100, K.104 Chain F: K.410, T.579 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:T.579, F:T.579, B:K.100, F:K.410, F:K.410 Salt bridges: F:K.410, B:K.564 5LS-GLC-PDX.7: 6 residues within 4Å: Chain C: S.94, G.96, K.100, K.104, P.105, E.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.94, C:K.104, C:E.106, C:E.106 Salt bridges: C:K.100 5LS-GLC-PDX.8: 6 residues within 4Å: Chain C: L.555, R.558, H.587, Q.590, S.591, R.594 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:K.583, C:R.594 Hydrogen bonds: C:R.558, C:R.558, C:Q.590, C:S.591, C:R.594 5LS-GLC-PDX.10: 5 residues within 4Å: Chain D: R.558, K.583, H.587, Q.590, R.594 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.558, D:R.558, D:R.558, D:R.558, D:R.594 Salt bridges: D:K.583, D:H.587, D:H.587, D:R.594 5LS-GLC-PDX.11: 6 residues within 4Å: Chain E: P.105, E.106, E.556, Q.557, I.560, K.564 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.106, E:Q.557, E:E.106, E:E.556 Salt bridges: E:K.564 5LS-GLC-PDX.12: 7 residues within 4Å: Chain E: L.551, R.558, K.583, H.587, Q.590, S.591, R.594 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:K.583, E:R.594 Hydrogen bonds: E:R.558, E:R.558, E:Q.590, E:R.594 5LS-GLC-PDX.13: 5 residues within 4Å: Chain F: G.96, K.100, K.104, Q.557 Ligands: 5TL.20 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:Q.557, F:Q.557, F:S.94 Salt bridges: D:K.410 5LS-GLC-PDX.14: 5 residues within 4Å: Chain F: R.558, H.587, Q.590, S.591, R.594 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:H.587, F:R.594, F:R.594 Hydrogen bonds: F:R.558, F:R.558, F:S.591

2 x 5LS- 5TJ- 5TM- 5TJ- Z4K- 5TK- 5TH: [(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate-(1-6)-(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-5-oxidanylsulfanyloxy-oxane-2,3,4-triol-(1-6)-2-O-sulfo-alpha-D-glucopyranose-(1-6)-[(2R,3R,4R,5R,6S)-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate-(1-6)-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-2,5-bis(oxidanyl)-4-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate-(1-6)-[(2R,3R,4R,5R,6S)-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate-(1-6)-2,4-di-O-sulfo-alpha-D-glucopyranose

5LS-5TJ-5TM-5TJ-Z4K-5TK-5TH.3: 6 residues within 4Å: Chain A: F.440, R.444, R.547 Chain B: R.444, R.546, R.547 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.444, A:R.547, A:R.547 Salt bridges: B:R.444, A:K.541 5LS-5TJ-5TM-5TJ-Z4K-5TK-5TH.9: 6 residues within 4Å: Chain C: F.440, R.444, R.546, R.547 Chain D: R.444, R.547 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.444, D:R.547, C:R.444, C:R.547 Salt bridges: C:R.444, C:R.547

6 x 5TL: 2-azanyl-5-phenyl-3-(4-sulfamoylphenyl)benzamide(Non-covalent)

5TL.15: 14 residues within 4Å: Chain A: L.16, G.17, T.18, V.24, M.90, E.91, Y.92, C.93, G.96, D.97, V.146, I.159, D.160 Ligands: 5LS-GLC-PDX.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.16, A:L.16, A:V.24, A:D.97, A:I.159, A:D.160 Hydrogen bonds: A:E.91, A:C.93, A:C.93, A:D.97, A:D.97 5TL.16: 13 residues within 4Å: Chain B: L.16, T.18, V.24, A.37, M.90, E.91, Y.92, C.93, G.96, D.97, V.146, I.159, D.160 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.16, B:L.16, B:V.24, B:D.97, B:V.146, B:I.159, B:D.160 Hydrogen bonds: B:E.91, B:C.93, B:C.93, B:D.97 5TL.17: 14 residues within 4Å: Chain C: L.16, G.17, T.18, V.24, A.37, M.90, E.91, Y.92, C.93, G.96, D.97, V.146, I.159, D.160 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.16, C:L.16, C:V.24, C:V.146, C:I.159, C:D.160 Hydrogen bonds: C:E.91, C:C.93, C:C.93, C:D.97 5TL.18: 13 residues within 4Å: Chain D: L.16, T.18, V.24, A.37, M.90, E.91, Y.92, C.93, G.96, D.97, V.146, I.159, D.160 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.16, D:L.16, D:V.24, D:D.97, D:V.146, D:I.159, D:D.160 Hydrogen bonds: D:E.91, D:C.93, D:C.93, D:D.97 5TL.19: 14 residues within 4Å: Chain E: L.16, G.17, T.18, V.24, A.37, M.90, E.91, Y.92, C.93, G.96, D.97, V.146, I.159, D.160 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:L.16, E:L.16, E:V.24, E:D.97, E:V.146, E:I.159, E:D.160 Hydrogen bonds: E:E.91, E:C.93, E:C.93, E:D.97 5TL.20: 14 residues within 4Å: Chain F: L.16, T.18, V.24, A.37, M.90, E.91, Y.92, C.93, G.96, D.97, V.146, I.159, D.160 Ligands: 5LS-GLC-PDX.13 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:L.16, F:L.16, F:V.24, F:D.97, F:V.146, F:I.159, F:D.160 Hydrogen bonds: F:E.91, F:C.93, F:C.93, F:D.97, F:D.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polley, S. et al., Structural Basis for the Activation of IKK1/ alpha. Cell Rep (2016)

Release Date

2016-11-02

Peptides

Inhibitor of nuclear factor kappa-B kinase subunit alpha: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

Inhibitor of nuclear factor kappa-B kinase subunit alpha

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