SMTL ID : 4xvu.1

Structure of Get3 bound to the transmembrane domain of Nyv1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-4-4-4-2-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 25 residues within 4Å: Chain A: G.27, G.28, V.29, G.30, K.31, T.32, T.33, N.57, P.169, N.272, Q.273, P.315, L.316, C.317, G.319, I.321, F.330 Chain B: K.26, G.27, I.243, E.245, F.246, L.247, R.291 Ligands: MG.2 23 PLIP interactions: 14 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:G.28, A:V.29, A:G.30, A:K.31, A:T.32, A:T.33, A:T.33, A:N.57, A:N.272, A:N.272, A:C.317, B:G.27, B:E.245, B:E.245, B:R.291 Water bridges: A:N.61, B:K.26, B:K.26 Salt bridges: A:K.31, A:K.31, B:K.26, B:K.26, B:K.26 ATP.4: 25 residues within 4Å: Chain A: K.26, G.27, I.243, E.245, F.246, L.247, R.291 Chain B: K.26, G.27, G.28, V.29, G.30, K.31, T.32, T.33, N.57, P.169, N.272, Q.273, P.315, L.316, C.317, I.321, F.330 Ligands: MG.5 24 PLIP interactions: 9 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:G.27, A:E.245, A:E.245, B:G.28, B:V.29, B:G.30, B:K.31, B:T.32, B:T.33, B:T.33, B:N.57, B:N.272, B:N.272, B:C.317 Water bridges: A:K.26, A:K.26, A:K.26, B:T.32, B:T.32 Salt bridges: A:K.26, A:K.26, A:K.26, B:K.31, B:K.31 ATP.6: 26 residues within 4Å: Chain G: K.26, G.27, G.28, V.29, G.30, K.31, T.32, T.33, N.57, P.169, N.272, Q.273, P.315, L.316, C.317, G.319, I.321, F.330 Chain H: K.26, G.27, I.243, E.245, F.246, L.247, R.291 Ligands: MG.7 25 PLIP interactions: 10 interactions with chain H, 15 interactions with chain G Hydrogen bonds: H:G.27, H:E.245, H:E.245, H:R.291, G:G.28, G:V.29, G:G.30, G:K.31, G:T.32, G:T.32, G:T.33, G:T.33, G:N.57, G:N.272, G:N.272, G:C.317 Water bridges: H:K.26, H:K.26, H:R.291, G:T.32 Salt bridges: H:K.26, H:K.26, H:K.26, G:K.31, G:K.31 ATP.9: 24 residues within 4Å: Chain G: K.26, G.27, I.243, E.245, L.247, S.248, R.291 Chain H: G.27, G.28, V.29, G.30, K.31, T.32, T.33, N.57, P.169, N.272, Q.273, P.315, L.316, C.317, I.321, F.330 Ligands: MG.10 27 PLIP interactions: 18 interactions with chain H, 9 interactions with chain G Hydrogen bonds: H:K.26, H:G.28, H:V.29, H:G.30, H:K.31, H:T.32, H:T.33, H:T.33, H:N.57, H:N.272, H:N.272, H:Q.273, H:C.317, G:G.27, G:R.291 Water bridges: H:K.31, H:K.31, H:I.321, G:K.26, G:K.26, G:L.247, G:E.251 Salt bridges: H:K.31, H:K.31, G:K.26, G:K.26, G:K.26

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.31, T.32, N.57, N.61 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.32, H2O.1, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain B: K.31, T.32, N.57, N.61 Ligands: ATP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.32, H2O.3, H2O.3, H2O.4 MG.7: 5 residues within 4Å: Chain G: K.31, T.32, N.57, N.61 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:T.32, H2O.18, H2O.19, H2O.20 MG.10: 5 residues within 4Å: Chain H: K.31, T.32, N.57, N.61 Ligands: ATP.9 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:T.32, H2O.22, H2O.22, H2O.23

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.285, R.287, C.288 Chain B: C.285, C.288 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.285, B:C.288, A:C.285, A:C.288 ZN.8: 4 residues within 4Å: Chain G: C.285, C.288 Chain H: C.285, C.288 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H Metal complexes: G:C.285, G:C.288, H:C.285, H:C.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mateja, A. et al., Protein targeting. Structure of the Get3 targeting factor in complex with its membrane protein cargo. Science (2015)

Release Date

2015-03-18

Peptides

ATPase GET3: ABGH
Antibody heavy chain: CEIK
Antibody light chain: DFJL
Nyv1 TMD: MN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

G
G

H
H

C
C

E
E

I
I

K
K

D
D

F
F

J
J

L
L

M
g

N
a

ATPase GET3

Antibody heavy chain

Antibody light chain

Nyv1 TMD

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