SMTL ID : 5ebz.1 (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: 2 residues within 4Å: Chain A: K.100, K.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.100, A:K.100, A:K.104, A:K.104 5LS-GLC-PDX.2: 5 residues within 4Å: Chain A: 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, A:R.558, A:R.558, A:Q.590 Salt bridges: A:H.587, A:R.594 5LS-GLC-PDX.4: 5 residues within 4Å: Chain B: K.104, E.106, K.564 Chain F: K.410, T.579 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:T.579, B:K.564 Salt bridges: F:K.410, B:K.104 5LS-GLC-PDX.5: 7 residues within 4Å: Chain B: L.551, R.558, V.586, H.587, Q.590, S.591, R.594 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.558, B:H.587, B:H.587 Hydrogen bonds: B:Q.590, B:Q.590 5LS-GLC-PDX.6: 5 residues within 4Å: Chain C: K.100, K.104, P.105, E.106, Q.557 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.100, C:E.106, C:Q.557 5LS-GLC-PDX.7: 6 residues within 4Å: Chain C: R.558, K.583, H.587, Q.590, S.591, R.594 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.558, C:R.558, C:Q.590, C:R.594 Salt bridges: C:R.558, C:H.587, C:H.587 5LS-GLC-PDX.9: 4 residues within 4Å: Chain D: S.94, K.100, P.105, E.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.94, D:K.104 5LS-GLC-PDX.10: 6 residues within 4Å: Chain D: L.555, 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:Q.590 Salt bridges: D:K.583, D:H.587, D:R.594 5LS-GLC-PDX.11: 4 residues within 4Å: Chain D: K.410 Chain F: K.100, K.104 Ligands: 5TL.20 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Salt bridges: D:K.410, D:K.410, F:K.104 5LS-GLC-PDX.12: 6 residues within 4Å: Chain E: K.100, K.104, P.105, E.106, Q.557, K.564 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.564 Hydrogen bonds: E:K.100, E:K.104, E:Q.557, E:Q.557 5LS-GLC-PDX.13: 6 residues within 4Å: Chain E: R.558, K.583, H.587, Q.590, S.591, R.594 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.558, E:R.558, E:K.583, E:K.583, E:H.587, E:Q.590, E:S.591 Salt bridges: E:R.594 5LS-GLC-PDX.14: 6 residues within 4Å: Chain F: R.558, K.583, H.587, Q.590, S.591, R.594 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.558, F:R.558, F:R.558, F:H.587, F:Q.590, F:S.591 Salt bridges: F:R.594, F:R.594

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: 9 residues within 4Å: Chain A: R.444, K.541, R.546, R.547 Chain B: R.444, Q.540, K.541, Y.544, R.547 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.444, B:R.444, B:K.541 Salt bridges: B:R.444, B:R.444, B:R.547, A:R.444, A:R.547 5LS-5TJ-5TM-5TJ-Z4K-5TK-5TH.8: 10 residues within 4Å: Chain C: R.444, Q.540, Y.544, R.547 Chain D: F.440, R.444, Q.540, K.541, Y.544, R.547 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:R.444, D:R.444, C:R.444, C:R.444, C:R.444, C:Q.540, C:Y.544, C:Y.544, C:R.547 Salt bridges: D:R.444, D:R.444, D:R.547, D:K.541

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

5TL.15: 12 residues within 4Å: Chain A: L.16, T.18, V.24, 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 A Hydrophobic interactions: A:L.16, A:L.16, A:V.24, A:D.97, A:V.146, A:I.159, A:D.160 Hydrogen bonds: A:E.91, A:C.93, A:C.93, 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: 12 residues within 4Å: Chain C: L.16, G.17, T.18, V.24, M.90, E.91, Y.92, C.93, 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: 13 residues within 4Å: Chain E: 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 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: 13 residues within 4Å: Chain D: D.408, K.410, I.411 Chain F: L.16, Y.92, C.93, S.94, G.96, D.97, R.99, V.146, I.159 Ligands: 5LS-GLC-PDX.11 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.16, F:D.97, F:V.146, F:I.159 Hydrogen bonds: F:C.93

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
A

B
B

C
C

D
D

E
E

F
F

Inhibitor of nuclear factor kappa-B kinase subunit alpha

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