SMTL ID : 6gy5.1

Crystal structure of the kelch domain of human KLHL20 in complex with DAPK1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: E.43, W.44 Ligand excluded by PLIP

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: W.25, F.261, Y.266, L.291 Chain B: L.6, V.7, A.8, K.9, Y.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:K.9, B:Y.10 Hydrogen bonds: A:Y.266 EDO.3: 3 residues within 4Å: Chain A: F.113, R.131, P.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.131, A:R.131, A:P.181 EDO.4: 6 residues within 4Å: Chain A: G.111, G.112, F.113, D.133, P.134, K.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.133 EDO.5: 5 residues within 4Å: Chain A: P.172, L.173, N.174, T.175, R.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.174, A:N.174, A:R.195 EDO.6: 10 residues within 4Å: Chain A: N.79, S.80, V.81, E.82, S.93, D.94, V.95, A.96, P.97 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.81, A:V.81 Water bridges: A:S.80 EDO.7: 6 residues within 4Å: Chain A: S.93, D.94, V.95, A.96, N.137 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.137 Water bridges: A:S.93 EDO.8: 2 residues within 4Å: Chain A: N.127, S.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.127 Water bridges: A:R.148 EDO.9: 5 residues within 4Å: Chain A: T.240, T.279, W.280, R.281, L.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.282 Water bridges: A:T.279 EDO.10: 12 residues within 4Å: Chain A: A.21, G.245, G.247, V.258, G.259, M.286, R.290, L.291, G.292, G.293, G.294, V.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.245, A:G.293, A:G.294

14 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain A: I.31, S.32, S.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.32, A:S.33 Water bridges: A:A.30, A:S.32 NA.12: 4 residues within 4Å: Chain A: S.60, V.61, G.296, V.297 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.61, A:V.297 Water bridges: A:V.59, A:S.60, A:S.60, A:S.60, A:V.61, A:V.295, A:V.297 NA.13: 4 residues within 4Å: Chain A: F.160, N.180, E.183, H.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.180 Water bridges: A:R.178 NA.14: 5 residues within 4Å: Chain A: G.193, E.224, W.233, S.234, P.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.193, A:W.233 NA.15: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.195 NA.16: 2 residues within 4Å: Chain A: T.194, R.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.195 Water bridges: A:G.193, A:R.195, A:D.215, A:D.215 NA.17: 2 residues within 4Å: Chain A: T.265, Y.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.266, A:Y.266 NA.18: 6 residues within 4Å: Chain A: S.104, Q.120, H.198 Chain B: P.4, D.5, L.6 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.5, B:L.6, A:S.104, A:S.104, A:Q.120 NA.19: 2 residues within 4Å: Chain A: T.147, R.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148 Water bridges: A:S.146 NA.20: 2 residues within 4Å: Chain A: S.76, Y.77 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.77 Water bridges: A:S.75, A:S.76, A:Y.77 NA.21: 3 residues within 4Å: Chain A: K.52, R.53, D.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.52, A:R.53 NA.22: 3 residues within 4Å: Chain A: K.52, L.78, S.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.80, A:S.80 Water bridges: A:K.52, A:S.80 NA.23: 2 residues within 4Å: Chain A: Y.288, R.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.289 Water bridges: A:R.289 NA.24: 5 residues within 4Å: Chain A: S.167, T.170, S.171, P.172, K.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.167, A:K.197, A:K.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Structural Basis for Recruitment of DAPK1 to the KLHL20 E3 Ligase. Structure (2019)

Release Date

2018-08-08

Peptides

Kelch-like protein 20: A
Death-associated protein kinase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
U

Kelch-like protein 20

Death-associated protein kinase 1