SMTL ID : 6chs.1

Cdc48-Npl4 complex in the presence of ATP-gamma-S

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-6-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.160, H.162, M.167, C.168, C.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.160, A:H.162, A:C.168, A:C.171 ZN.2: 5 residues within 4Å: Chain A: C.227, H.231, C.239, K.241, C.242 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.227, A:H.231, A:C.239, A:C.242

12 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.3: 17 residues within 4Å: Chain B: I.222, P.263, G.264, T.265, G.266, K.267, T.268, L.269, D.320, N.364, I.396, H.400, G.424, S.425 Chain G: R.375, F.376 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.264, B:T.265, B:T.265, B:G.266, B:K.267, B:T.268, B:T.268, B:L.269, B:G.424, B:S.425 Salt bridges: B:K.267, B:K.267 AGS.4: 15 residues within 4Å: Chain B: P.537, G.538, T.539, G.540, K.541, T.542, M.543, N.641, I.673, Q.677, G.701, A.702 Chain G: R.652, P.653 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.538, B:T.539, B:G.540, B:K.541, B:T.542, B:T.542, B:N.641, B:G.701, B:A.702 Salt bridges: B:K.541 AGS.7: 16 residues within 4Å: Chain B: R.375, F.376 Chain C: I.222, P.263, G.264, T.265, G.266, K.267, T.268, L.269, N.364, I.396, H.400, G.424, S.425 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.264, C:T.265, C:T.265, C:G.266, C:K.267, C:T.268, C:T.268, C:L.269, C:G.424, C:S.425 Salt bridges: C:K.267, C:K.267 AGS.8: 15 residues within 4Å: Chain B: R.652 Chain C: P.536, P.537, G.538, T.539, G.540, K.541, T.542, M.543, N.641, I.673, Q.677, G.701, A.702 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.538, C:T.539, C:G.540, C:K.541, C:T.542, C:T.542, C:G.701, C:A.702 Salt bridges: C:K.541 AGS.11: 17 residues within 4Å: Chain C: R.375, F.376 Chain D: I.222, P.263, G.264, T.265, G.266, K.267, T.268, L.269, D.320, N.364, I.396, H.400, G.424, S.425 Ligands: MG.13 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.264, D:T.265, D:T.265, D:G.266, D:G.266, D:K.267, D:T.268, D:L.269, D:G.424, D:S.425 Salt bridges: D:K.267, D:K.267 AGS.12: 15 residues within 4Å: Chain C: R.652 Chain D: G.497, P.537, G.538, T.539, G.540, K.541, T.542, M.543, N.641, I.673, Q.677, G.701, A.702 Ligands: MG.14 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.497, D:G.497, D:G.538, D:T.539, D:G.540, D:K.541, D:T.542, D:T.542, D:N.641, D:Q.677, D:G.701, D:A.702 Salt bridges: D:K.541 AGS.15: 16 residues within 4Å: Chain D: R.375, F.376 Chain E: I.222, P.263, G.264, T.265, G.266, K.267, T.268, L.269, N.364, I.396, H.400, G.424, S.425 Ligands: MG.17 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.264, E:T.265, E:T.265, E:G.266, E:K.267, E:T.268, E:T.268, E:T.268, E:L.269, E:N.364, E:G.424, E:S.425 Salt bridges: E:K.267 AGS.16: 16 residues within 4Å: Chain D: R.652, P.653 Chain E: P.536, P.537, G.538, T.539, G.540, K.541, T.542, M.543, N.641, I.673, Q.677, G.701, A.702 Ligands: MG.18 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:P.536, E:G.538, E:T.539, E:G.540, E:K.541, E:T.542, E:T.542, E:N.641, E:G.701, E:A.702 Salt bridges: E:K.541 AGS.19: 17 residues within 4Å: Chain E: R.375, F.376 Chain F: I.222, P.263, G.264, T.265, G.266, K.267, T.268, L.269, D.320, N.364, I.396, H.400, G.424, S.425 Ligands: MG.21 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.264, F:T.265, F:T.265, F:G.266, F:G.266, F:K.267, F:T.268, F:L.269, F:G.424, F:S.425 Salt bridges: F:K.267, F:K.267 AGS.20: 14 residues within 4Å: Chain F: P.536, P.537, G.538, T.539, G.540, K.541, T.542, M.543, N.641, I.673, Q.677, G.701, A.702 Ligands: MG.22 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.497, F:G.497, F:P.536, F:G.538, F:T.539, F:G.540, F:K.541, F:T.542, F:N.641, F:Q.677, F:G.701, F:A.702 Salt bridges: F:K.541 AGS.23: 15 residues within 4Å: Chain F: F.376 Chain G: I.222, G.223, P.263, G.264, T.265, G.266, K.267, T.268, L.269, I.396, H.400, G.424, S.425 Ligands: MG.25 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.223, G:G.223, G:G.264, G:T.265, G:T.265, G:G.266, G:K.267, G:T.268, G:L.269, G:G.424 Salt bridges: G:K.267 AGS.24: 18 residues within 4Å: Chain F: R.652 Chain G: D.495, I.496, G.497, P.537, G.538, T.539, G.540, K.541, T.542, M.543, N.641, I.673, Q.677, G.701, A.702, A.705 Ligands: MG.26 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.497, G:G.497, G:G.538, G:T.539, G:G.540, G:K.541, G:T.542, G:N.641, G:Q.677 Salt bridges: G:K.541

12 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: T.268, D.320 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.268 MG.6: 3 residues within 4Å: Chain B: T.542, D.594 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.542 MG.9: 3 residues within 4Å: Chain C: T.268, D.320 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.268 MG.10: 3 residues within 4Å: Chain C: T.542, D.594 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.542 MG.13: 3 residues within 4Å: Chain D: T.268, D.320 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.268 MG.14: 3 residues within 4Å: Chain D: T.542, D.594 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.542 MG.17: 3 residues within 4Å: Chain E: T.268, D.320 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.320 MG.18: 3 residues within 4Å: Chain E: T.542, D.594 Ligands: AGS.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.542 MG.21: 3 residues within 4Å: Chain F: T.268, D.320 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.268 MG.22: 2 residues within 4Å: Chain F: T.542 Ligands: AGS.20 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.542 MG.25: 3 residues within 4Å: Chain G: T.268, D.320 Ligands: AGS.23 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.268 MG.26: 2 residues within 4Å: Chain G: T.542 Ligands: AGS.24 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bodnar, N.O. et al., Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-07-04

Peptides

Npl4: A
Putative cell division control protein: BCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
I

D
J

E
D

F
E

G
F

Npl4

Putative cell division control protein