SMTL ID : 6ap1.1

Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-12-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: D.35, V.36, A.37, G.77, T.78, G.79, K.80, S.81, Y.82, G.237, S.238, A.241 Chain B: N.162, R.189 Ligands: BEF.2, MG.3 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.37, A:G.77, A:T.78, A:G.79, A:K.80, A:S.81, A:Y.82, B:N.162 Salt bridges: A:K.80, B:R.189, B:R.189 ADP.4: 15 residues within 4Å: Chain B: D.35, A.37, G.77, T.78, G.79, K.80, S.81, Y.82, M.208, G.237, S.238 Chain C: N.162, R.189 Ligands: BEF.5, MG.6 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:N.162, B:A.37, B:A.37, B:G.77, B:T.78, B:G.79, B:K.80, B:S.81, B:Y.82 Salt bridges: C:R.189, C:R.189, B:K.80 ADP.7: 15 residues within 4Å: Chain C: D.35, V.36, A.37, G.77, T.78, G.79, K.80, S.81, Y.82, G.237, S.238 Chain D: N.162, R.189 Ligands: BEF.8, MG.9 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:N.162, C:A.37, C:G.77, C:T.78, C:T.78, C:G.79, C:K.80, C:S.81, C:Y.82 Salt bridges: D:R.189, D:R.189, C:K.80 ADP.10: 14 residues within 4Å: Chain D: D.35, A.37, P.76, G.77, T.78, G.79, K.80, S.81, Y.82, M.208, G.237, S.238 Chain E: R.189 Ligands: MG.11 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:A.37, D:A.37, D:G.77, D:T.78, D:G.79, D:K.80, D:S.81, D:S.81, D:Y.82 Salt bridges: D:K.80, E:R.189, E:R.189 ADP.12: 11 residues within 4Å: Chain E: A.37, P.76, G.77, T.78, G.79, K.80, S.81, Y.82, M.208, G.237, S.238 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:A.37, E:A.37, E:G.77, E:T.78, E:G.79, E:K.80, E:S.81, E:Y.82, E:G.237 Salt bridges: E:K.80

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

BEF.2: 10 residues within 4Å: Chain A: P.75, P.76, G.77, T.78, K.80, S.81, N.178 Chain B: R.189 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 10 residues within 4Å: Chain B: P.75, P.76, G.77, K.80, S.81, N.178 Chain C: R.189, R.190 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.8: 10 residues within 4Å: Chain C: P.75, P.76, G.77, T.78, K.80, S.81 Chain D: R.189, R.190 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.81 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.81 MG.6: 3 residues within 4Å: Chain B: S.81 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.81 MG.9: 3 residues within 4Å: Chain C: S.81 Ligands: ADP.7, BEF.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.81 MG.11: 3 residues within 4Å: Chain D: S.81, D.133 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, H. et al., The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Elife (2017)

Release Date

2017-12-06

Peptides

Vacuolar protein sorting-associated protein 4,Protein hcp1: ABCDEG
ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2: F
Vacuolar protein sorting-associated protein VTA1: HIJKLMNOPQRS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

G
F

F
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

Vacuolar protein sorting-associated protein 4,Protein hcp1

ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2

Vacuolar protein sorting-associated protein VTA1

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