SMTL ID : 8kg2.1

Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-12-12-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: D.185, I.186, G.187, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 Chain F: R.339, F.340 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain F 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:T.232, A:T.232, A:L.233, F:R.339 Salt bridges: A:K.231 ADP.2: 16 residues within 4Å: Chain B: 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, A.392 Chain D: R.339, F.340 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.187, B:P.226, 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, B:G.388 Salt bridges: B:K.231, D:R.339 ADP.3: 17 residues within 4Å: Chain A: R.339, F.340 Chain C: D.185, I.186, G.187, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.187, C:P.226, C:G.228, C:T.229, C:T.229, C:T.229, C:G.230, C:K.231, C:T.232, C:T.232, C:L.233, A:R.339 Salt bridges: C:K.231, A:R.339 ADP.4: 16 residues within 4Å: Chain C: F.340 Chain D: D.185, I.186, G.187, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.187, D:P.226, D:G.228, D:T.229, D:T.229, D:G.230, D:K.231, D:T.232, D:T.232, D:L.233 Salt bridges: D:K.231 ADP.5: 17 residues within 4Å: Chain B: R.339, F.340 Chain E: D.185, I.186, G.187, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.187, E:G.228, E:T.229, 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, B:R.339 ADP.6: 16 residues within 4Å: Chain E: R.339, F.340 Chain F: 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, A.392 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.187, F:G.228, F:T.229, F:T.229, F:G.230, F:K.231, F:T.232, F:T.232, F:T.232, F:L.233, F:G.388, E:R.339 Salt bridges: F:K.231, E:R.339 ADP.7: 19 residues within 4Å: Chain M: D.185, I.186, G.187, C.189, P.226, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 Chain R: R.339, F.340 14 PLIP interactions: 13 interactions with chain M, 1 interactions with chain R Hydrogen bonds: M:G.187, M:P.226, M:G.228, M:T.229, M:T.229, M:T.229, M:G.230, M:K.231, M:T.232, M:T.232, M:T.232, M:L.233 Salt bridges: M:K.231, R:R.339 ADP.8: 18 residues within 4Å: Chain N: D.185, I.186, G.187, C.189, P.226, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 Chain P: R.339, F.340 15 PLIP interactions: 14 interactions with chain N, 1 interactions with chain P Hydrogen bonds: N:G.187, N:P.226, N:G.228, N:T.229, N:T.229, N:T.229, N:G.230, N:K.231, N:T.232, N:T.232, N:T.232, N:L.233, N:G.388, P:R.339 Salt bridges: N:K.231 ADP.9: 19 residues within 4Å: Chain M: R.339, F.340 Chain O: D.185, I.186, G.187, C.189, P.226, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 14 PLIP interactions: 13 interactions with chain O, 1 interactions with chain M Hydrogen bonds: O:G.187, O:P.226, O:G.228, O:T.229, O:T.229, O:T.229, O:G.230, O:K.231, O:T.232, O:T.232, O:T.232, O:L.233, M:R.339 Salt bridges: O:K.231 ADP.10: 16 residues within 4Å: Chain O: R.339, F.340 Chain P: 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, A.392 13 PLIP interactions: 12 interactions with chain P, 1 interactions with chain O Hydrogen bonds: P:G.187, P:G.187, P:P.226, P:G.228, P:T.229, P:T.229, P:G.230, P:K.231, P:T.232, P:T.232, P:L.233 Salt bridges: P:K.231, O:R.339 ADP.11: 16 residues within 4Å: Chain N: R.339 Chain Q: D.185, I.186, G.187, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 12 PLIP interactions: 11 interactions with chain Q, 1 interactions with chain N Hydrogen bonds: Q:G.187, Q:P.226, Q:G.228, Q:T.229, Q:T.229, Q:G.230, Q:K.231, Q:T.232, Q:T.232, Q:L.233 Salt bridges: Q:K.231, N:R.339 ADP.12: 19 residues within 4Å: Chain Q: R.339, F.340 Chain R: D.185, I.186, G.187, C.189, P.226, P.227, G.228, T.229, G.230, K.231, T.232, L.233, I.360, H.364, G.388, A.389, A.392 13 PLIP interactions: 12 interactions with chain R, 1 interactions with chain Q Hydrogen bonds: R:G.187, R:P.226, R:G.228, R:T.229, R:T.229, R:G.230, R:K.231, R:T.232, R:T.232, R:T.232, R:L.233, Q:R.339 Salt bridges: R:K.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, W., Crystal Structure of p97-N/D1 Hexamer Complexed with FAF1 UBX Domain. J. Korean Chem. Soc. (2024)

Release Date

2024-05-29

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEFMNOPQR
FAS-associated factor 1: GHIJKLSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

M
G

N
H

O
I

P
J

Q
K

R
L

G
M

H
N

I
O

J
P

K
Q

L
R

S
S

T
T

U
U

V
V

W
W

X
X

Transitional endoplasmic reticulum ATPase

FAS-associated factor 1