SMTL ID : 8hrz.1

Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-12-12-mer

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: D.185, I.186, G.187, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.187, A:G.228, A:T.229, A:T.229, A:T.229, A:G.230, A:K.231, A:T.232, A:L.233 Salt bridges: A:K.231 ADP.2: 14 residues within 4Å: Chain B: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.187, B:G.228, B:T.229, B:T.229, B:G.230, B:K.231, B:T.232, B:T.232, B:T.232, B:L.233 Salt bridges: B:K.231 ADP.3: 15 residues within 4Å: Chain B: R.339 Chain C: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.187, C:G.228, C:T.229, C:T.229, C:G.230, C:K.231, C:T.232, C:T.232, C:T.232, C:L.233, B:R.339, B:R.339 Salt bridges: C:K.231 ADP.4: 14 residues within 4Å: Chain C: R.339 Chain D: D.185, I.186, G.187, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.187, D:G.228, D:T.229, D:T.229, D:G.230, D:K.231, D:T.232, D:T.232, D:T.232, D:L.233, C:R.339 Salt bridges: D:K.231, C:R.339 ADP.5: 13 residues within 4Å: Chain E: D.185, I.186, G.187, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.187, E:G.187, E:G.228, E:T.229, E:G.230, E:K.231, E:T.232, E:T.232, E:T.232, E:L.233 Salt bridges: E:K.231 ADP.6: 14 residues within 4Å: Chain F: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.187, F:G.187, F:G.228, F:T.229, F:G.230, F:K.231, F:T.232, F:T.232, F:T.232, F:L.233 Salt bridges: F:K.231 ADP.7: 13 residues within 4Å: Chain G: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:G.187, G:G.187, G:G.228, G:T.229, G:T.229, G:G.230, G:K.231, G:T.232, G:T.232, G:T.232, G:L.233 Salt bridges: G:K.231 ADP.8: 14 residues within 4Å: Chain H: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:G.187, H:G.228, H:T.229, H:T.229, H:G.230, H:K.231, H:T.232, H:T.232, H:L.233 Salt bridges: H:K.231 ADP.9: 14 residues within 4Å: Chain I: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:G.187, I:G.228, I:T.229, I:T.229, I:G.230, I:K.231, I:T.232, I:T.232, I:T.232, I:L.233 Salt bridges: I:K.231 ADP.10: 14 residues within 4Å: Chain J: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.187, J:G.228, J:T.229, J:T.229, J:G.230, J:K.231, J:T.232, J:T.232, J:T.232, J:L.233 Salt bridges: J:K.231 ADP.11: 15 residues within 4Å: Chain J: R.339 Chain K: D.185, I.186, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 13 PLIP interactions: 12 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:G.187, K:G.228, K:T.229, K:T.229, K:T.229, K:G.230, K:K.231, K:T.232, K:T.232, K:T.232, K:L.233 Salt bridges: K:K.231, J:R.339 ADP.12: 13 residues within 4Å: Chain L: D.185, I.186, G.187, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.187, L:G.228, L:T.229, L:T.229, L:T.229, L:G.230, L:K.231, L:T.232, L:T.232, L:L.233 Salt bridges: L:K.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T.Q. et al., Crystal structure of the p97-N/D1 hexmaer in complex with six p47-UBX domains. J. Korean Chem. Soc. (2024)

Release Date

2023-12-20

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEFGHIJKL
NSFL1 cofactor p47: MNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
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

T
T

U
U

V
V

W
W

X
X

Transitional endoplasmic reticulum ATPase

NSFL1 cofactor p47