SMTL ID : 8u7c.1

Engineered NEMO minimal IKK-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-tetramer

Ligands

3 x TB: TERBIUM(III) ION(Non-covalent)

TB.1: 3 residues within 4Å: Chain A: E.42, E.45 Ligands: BTB.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:E.45, A:E.45, H2O.1 TB.11: 3 residues within 4Å: Chain D: E.28, E.31 Ligands: BTB.19 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.28, D:E.28, D:E.31, H2O.5 TB.12: 4 residues within 4Å: Chain D: E.10 Ligands: ER3.13, BTB.17, BTB.18 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.10, H2O.4

5 x 9JE: pentane-1,5-diol(Non-covalent)

9JE.2: 8 residues within 4Å: Chain A: F.51, A.54, R.55, V.58 Chain D: N.23, L.26, R.27, S.30 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:A.54, A:R.55 Hydrogen bonds: D:N.23, D:S.30 Water bridges: D:S.30 9JE.3: 8 residues within 4Å: Chain A: S.30, L.33, L.34, Q.37 Chain D: K.44, L.47, M.48, F.51 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.33, A:L.34, D:L.47 Hydrogen bonds: A:S.30, A:L.33 Water bridges: D:Q.52 9JE.7: 5 residues within 4Å: Chain B: S.30, L.33 Chain C: K.44, F.51 Chain D: F.36 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.33, C:K.44 Hydrogen bonds: B:S.30 9JE.9: 5 residues within 4Å: Chain B: N.23, R.27, S.30 Chain C: F.51, R.55 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.23, B:S.30, B:S.30, C:R.55 Hydrophobic interactions: C:F.51 9JE.15: 7 residues within 4Å: Chain A: N.23, L.26, R.27, S.30 Chain D: F.51, Q.52, R.55 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.51, A:L.26 Hydrogen bonds: D:Q.52, D:R.55 Water bridges: D:Q.52

5 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 4 residues within 4Å: Chain A: E.42, E.45 Ligands: TB.1, PRO.5 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.42, A:E.45 BTB.17: 7 residues within 4Å: Chain D: R.7, E.10, E.11, E.14 Ligands: TB.12, ER3.13, BTB.18 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.10, D:E.10, D:E.11, D:E.14 Water bridges: D:E.14 Salt bridges: D:E.14 BTB.18: 4 residues within 4Å: Chain D: E.10 Ligands: TB.12, ER3.13, BTB.17 2 PLIP interactions: 2 interactions with chain D Water bridges: D:E.10 Salt bridges: D:E.10 BTB.19: 4 residues within 4Å: Chain D: R.27, E.28, E.31 Ligands: TB.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.27, D:E.31 Water bridges: D:E.28, D:E.31 Salt bridges: D:E.28, D:E.31 BTB.20: 3 residues within 4Å: Chain D: E.42, E.45 Ligands: YT3.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.45 Water bridges: D:E.42, D:E.42 Salt bridges: D:E.42, D:E.45

2 x PRO: PROLINE(Non-covalent)

PRO.5: 3 residues within 4Å: Chain A: E.45, F.46 Ligands: BTB.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:E.45, A:F.46 Hydrogen bonds: P.5, P.5 PRO.10: 4 residues within 4Å: Chain B: R.7, C.8, E.11 Chain D: N.12 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 2 Ligand-Ligand interactions Water bridges: B:E.4, B:C.8 Salt bridges: B:R.7 Hydrophobic interactions: D:N.12 Hydrogen bonds: P.10, P.10

2 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.6: 2 residues within 4Å: Chain B: E.42, E.45 No protein-ligand interaction detected (PLIP) YT3.14: 3 residues within 4Å: Chain D: E.42, E.45 Ligands: BTB.20 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 3 residues within 4Å: Chain A: E.53 Chain B: D.17, Q.21 No protein-ligand interaction detected (PLIP) PG4.16: 11 residues within 4Å: Chain A: K.44, L.47, F.51 Chain B: L.33, F.36, Q.40 Chain D: S.30, L.33, F.36, Q.37, Q.40 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.30, D:Q.40, D:Q.40

1 x ER3: ERBIUM (III) ION(Non-functional Binders)

ER3.13: 3 residues within 4Å: Ligands: TB.12, BTB.17, BTB.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kennedy, A.E. et al., The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition. Structure (2025)

Release Date

2025-01-22

Peptides

Engineered NEMO minimal IKK-binding domain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Engineered NEMO minimal IKK-binding domain