SMTL ID : 6ndy.1

Vps4 with Cyclic Peptide Bound in the Central Pore

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-5-1-mer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: D.34, V.35, A.36, G.76, T.77, G.78, K.79, S.80, Y.81, M.207, G.236, S.237, A.240 Chain B: N.161, R.188 Ligands: BEF.2, MG.3 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.36, A:A.36, A:G.76, A:T.77, A:G.78, A:K.79, A:S.80, B:N.161 Salt bridges: A:K.84, B:R.188, B:R.188 ADP.4: 16 residues within 4Å: Chain B: D.34, V.35, A.36, G.76, T.77, G.78, K.79, S.80, Y.81, G.236, S.237 Chain C: N.161, R.188, R.189 Ligands: BEF.5, MG.6 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain B Salt bridges: C:R.188, C:R.188, B:K.79 Hydrogen bonds: B:A.36, B:G.76, B:T.77, B:T.77, B:G.78, B:K.79, B:S.80, B:Y.81 ADP.7: 17 residues within 4Å: Chain C: D.34, V.35, A.36, L.38, G.76, T.77, G.78, K.79, S.80, Y.81, M.207, G.236, S.237 Chain D: N.161, R.188 Ligands: BEF.8, MG.9 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:A.36, C:G.76, C:T.77, C:T.77, C:G.78, C:K.79, C:S.80 Salt bridges: C:K.84, D:R.188, D:R.188 ADP.10: 16 residues within 4Å: Chain D: D.34, V.35, A.36, P.75, G.76, T.77, G.78, K.79, S.80, Y.81, M.207, G.236, S.237 Chain E: R.188, R.189 Ligands: MG.11 12 PLIP interactions: 3 interactions with chain E, 9 interactions with chain D Salt bridges: E:R.188, E:R.188, E:R.189, D:K.79 Hydrogen bonds: D:A.36, D:A.36, D:G.76, D:T.77, D:G.78, D:S.80, D:S.80, D:Y.81 ADP.12: 12 residues within 4Å: Chain E: D.34, V.35, A.36, G.76, T.77, G.78, K.79, S.80, Y.81, M.207, G.236, S.237 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.36, E:A.36, E:G.76, E:T.77, E:G.78, E:K.79, E:S.80, E:S.80, E:Y.81

3 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 11 residues within 4Å: Chain A: P.74, P.75, G.76, T.77, K.79, S.80, N.177 Chain B: R.188, R.189 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 9 residues within 4Å: Chain B: P.74, P.75, G.76, K.79, N.177 Chain C: R.188, R.189 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.8: 10 residues within 4Å: Chain C: P.74, P.75, G.76, T.77, K.79, N.177 Chain D: R.188, R.189 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.80, D.132 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.80 MG.6: 3 residues within 4Å: Chain B: S.80 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.80 MG.9: 3 residues within 4Å: Chain C: S.80 Ligands: ADP.7, BEF.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.80 MG.11: 3 residues within 4Å: Chain D: S.80, D.132 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, H. et al., Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases. Elife (2019)

Release Date

2019-08-21

Peptides

Vacuolar protein sorting-associated protein 4: ABCDE
Designed Cyclic Peptide: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

Vacuolar protein sorting-associated protein 4

Designed Cyclic Peptide

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