SMTL ID : 8bzl.1

Human 20S Proteasome in complex with peptide activator peptide BLM42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-6-mer

Ligands

54 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: R.66, R.70 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: Y.6, S.7, F.8 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: R.219, R.220 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: H.88, R.91 Chain H: K.116 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: T.69, P.104 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: N.69, E.70, Q.95 Chain J: N.72 Ligands: CL.9 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain C: L.98, P.104 Ligands: CL.8 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: V.26, I.161, G.162 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: R.86, L.114, R.117 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain E: I.31, K.32, I.170, G.171, S.174 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain F: K.30, C.148, I.161, G.162, S.165 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain F: C.148, S.150 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain 5: Y.12 Chain E: L.121, S.159 Chain F: L.77, T.78, A.79 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain G: V.31, I.166, G.167, R.170 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain H: K.102, Y.103 Chain O: Y.95 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain H: F.191, E.192, Q.193, T.197 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain I: T.44, A.89, G.90, G.171, S.172 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain I: N.123, R.124 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain J: R.66, R.70 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain L: T.60, G.106, G.188, S.189 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain L: S.77, T.89, N.234 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain L: Q.121, Y.125, R.128 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain K: K.29 Chain L: I.180, S.181 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain N: F.81, R.82, N.83, I.84 Ligand excluded by PLIP CL.38: 6 residues within 4Å: Chain N: R.80 Chain O: S.80, G.131, G.162, G.163 Ligands: CL.39 Ligand excluded by PLIP CL.39: 5 residues within 4Å: Chain N: Y.75, R.80 Chain O: P.149, M.150 Ligands: CL.38 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain N: M.88, R.89 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain O: T.65, R.79, A.83, Q.87 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain O: T.35, G.81, G.163, S.164 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain O: R.53, I.60, R.63, G.205, G.206 Ligand excluded by PLIP CL.46: 4 residues within 4Å: Chain P: S.7, F.8 Chain Q: S.2 Chain R: R.5 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain A: R.70, M.90 Chain P: V.100, Y.101 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain P: P.67, R.220 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain P: H.88, R.91 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain A: N.72 Chain Q: N.69, E.70, Q.95 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain R: R.95, E.99 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain R: V.26, I.161, G.162, A.165 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain S: I.31, I.170, G.171, S.174 Ligand excluded by PLIP CL.54: 5 residues within 4Å: Chain T: K.30, C.148, I.161, G.162, S.165 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain T: C.148, S.150, N.152, F.154 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain 1: Y.95 Chain V: K.102 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain W: T.44, G.171, S.172 Ligand excluded by PLIP CL.60: 3 residues within 4Å: Chain W: V.120, N.123, R.124 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain Y: T.60, G.106, G.188, S.189 Ligand excluded by PLIP CL.65: 3 residues within 4Å: Chain Y: Q.121, Y.125, R.128 Ligand excluded by PLIP CL.66: 3 residues within 4Å: Chain Y: S.77, T.89, N.234 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain X: K.29 Chain Y: I.180, S.181 Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain Y: D.213, L.214 Ligand excluded by PLIP CL.72: 4 residues within 4Å: Chain 0: F.81, R.82, N.83, I.84 Ligand excluded by PLIP CL.73: 6 residues within 4Å: Chain 0: R.80 Chain 1: S.80, G.131, G.162, G.163 Ligands: CL.74 Ligand excluded by PLIP CL.74: 5 residues within 4Å: Chain 0: Y.75, R.80 Chain 1: P.149, M.150 Ligands: CL.73 Ligand excluded by PLIP CL.75: 2 residues within 4Å: Chain 0: M.88, R.89 Ligand excluded by PLIP CL.77: 4 residues within 4Å: Chain 1: T.35, G.81, G.163, S.164 Ligand excluded by PLIP CL.78: 5 residues within 4Å: Chain 1: R.53, I.60, R.63, G.205, G.206 Ligand excluded by PLIP

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: V.175, D.178, S.181, D.205 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.175, A:D.178, A:S.181, H2O.2, H2O.2 MG.23: 3 residues within 4Å: Chain I: Q.134 Chain O: D.85, D.127 No protein-ligand interaction detected (PLIP) MG.24: 6 residues within 4Å: Chain I: R.62, I.206, D.209, L.210, S.212 Chain Z: D.241 5 PLIP interactions: 1 interactions with chain Z, 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: Z:D.241, I:I.206, I:D.209, I:S.212, H2O.117 MG.26: 3 residues within 4Å: Chain J: V.175, D.178, S.181 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:V.175, J:D.178, J:S.181, H2O.41, H2O.44 MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.34: 6 residues within 4Å: Chain A: D.205 Chain L: R.78, T.223, D.226, A.227, S.229 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: L:T.223, L:D.226, L:S.229, A:D.205, H2O.55 MG.61: 3 residues within 4Å: Chain 1: D.85, D.127 Chain W: Q.134 No protein-ligand interaction detected (PLIP) MG.62: 6 residues within 4Å: Chain M: D.241 Chain W: R.62, I.206, D.209, L.210, S.212 5 PLIP interactions: 3 interactions with chain W, 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: W:I.206, W:D.209, W:S.212, M:D.241, H2O.99 MG.63: 1 residues within 4Å: Chain X: P.97 No protein-ligand interaction detected (PLIP) MG.69: 6 residues within 4Å: Chain J: D.205 Chain Y: R.78, T.223, D.226, A.227, S.229 5 PLIP interactions: 1 interactions with chain J, 3 interactions with chain Y, 1 Ligand-Water interactions Metal complexes: J:D.205, Y:T.223, Y:D.226, Y:S.229, H2O.109

9 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 5 residues within 4Å: Chain A: R.66, E.97, K.98, Y.103 Chain X: D.90 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain X Hydrogen bonds: A:K.98, X:D.90 Water bridges: A:R.70, A:R.70, A:F.100, A:G.101 1PE.20: 7 residues within 4Å: Chain H: Y.103 Chain I: F.131, R.132, Q.134 Chain O: A.88, Y.124, L.128 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:Y.103, I:R.132 1PE.27: 5 residues within 4Å: Chain J: R.66, E.97, K.98 Chain K: D.90 Ligands: 1PE.28 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:K.98 Water bridges: J:R.70 1PE.28: 8 residues within 4Å: Chain I: L.101, Y.133, I.137 Chain J: Y.96, E.97, R.99, F.100 Ligands: 1PE.27 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:Y.133 Water bridges: J:Y.96 1PE.35: 7 residues within 4Å: Chain E: N.98, F.101 Chain L: W.114, L.117, Y.149 Chain M: Y.125, F.129 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.98 1PE.41: 6 residues within 4Å: Chain 1: T.56, G.57, Y.59 Chain N: Y.186, Y.189 Chain W: S.172 No protein-ligand interaction detected (PLIP) 1PE.58: 7 residues within 4Å: Chain 1: A.92, D.127, L.128 Chain V: Y.103 Chain W: F.131, R.132, Q.134 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:R.132 1PE.70: 7 residues within 4Å: Chain S: F.101 Chain Y: F.113, L.117, Y.149 Chain Z: Y.125, S.126, F.129 1 PLIP interactions: 1 interactions with chain Y Hydrogen bonds: Y:Y.149 1PE.76: 6 residues within 4Å: Chain 0: Y.186, Y.189 Chain I: G.171, S.172 Chain O: T.56 Chain Z: F.61 1 PLIP interactions: 1 interactions with chain 0 Hydrogen bonds: 0:Y.186

6 x K: POTASSIUM ION(Non-covalent)

K.19: 4 residues within 4Å: Chain H: T.14, Y.125, N.128, M.131 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:Y.125, H:N.128, H:M.131, H2O.31 K.36: 5 residues within 4Å: Chain M: A.211, D.214, T.217, D.241 Chain W: R.62 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:A.211 K.45: 4 residues within 4Å: Chain O: R.53, M.198, D.201, S.204 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:M.198, O:D.201, O:S.204, H2O.72, H2O.73 K.57: 4 residues within 4Å: Chain V: T.14, Y.125, N.128, M.131 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:Y.125, V:N.128, V:M.131 K.71: 4 residues within 4Å: Chain Z: A.211, D.214, V.215, T.217 3 PLIP interactions: 2 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: Z:A.211, Z:T.217, H2O.114 K.79: 4 residues within 4Å: Chain 1: R.53, M.198, D.201, S.204 3 PLIP interactions: 2 interactions with chain 1, 1 Ligand-Water interactions Metal complexes: 1:M.198, 1:S.204, H2O.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gizynska, M. et al., Peptidic, Blm10-based activators of human 20S proteasome in vitro and in cellulo enhance degradation of proteins connected with neurodegeneration. To Be Published

Release Date

2023-12-27

Peptides

Proteasome subunit beta type-3: AJ
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-4: CQ
Proteasome subunit alpha type-7: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-1: FT
Proteasome subunit alpha type-3: GU
Proteasome subunit alpha type-6: HV
Proteasome subunit beta type-7: IW
Proteasome subunit beta type-2: KX
Proteasome subunit beta type-5: LY
Proteasome subunit beta type-1: MZ
Proteasome subunit beta type-4: N0
Proteasome subunit beta type-6: O1
ARG-SER-TYR-TYR-SER: 234567

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

J
I

B
A

P
O

C
B

Q
P

D
C

R
Q

E
D

S
R

F
E

T
S

G
F

U
T

H
G

V
U

I
H

W
V

K
J

X
X

L
K

Y
Y

M
L

Z
Z

N
M

0
a

O
N

1
b

2
c

3
d

4
e

5
f

6
g

7
h

Proteasome subunit beta type-3

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-5

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit alpha type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-2

Proteasome subunit beta type-5

Proteasome subunit beta type-1

Proteasome subunit beta type-4

Proteasome subunit beta type-6

ARG-SER-TYR-TYR-SER

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