SMTL ID : 5nif.1

Yeast 20S proteasome in complex with Blm-pep activator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

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

CL.1: 2 residues within 4Å: Chain A: K.98 Chain G: D.114 Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain K: N.101 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain N: Q.135 Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain R: R.119 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain S: N.168 Ligand excluded by PLIP CL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain 1: K.48, Q.158 Ligand excluded by PLIP CL.41: 2 residues within 4Å: Chain 1: N.59, K.243 Ligand excluded by PLIP CL.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain N: N.59, E.73, K.243 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain Q: Y.122 No protein-ligand interaction detected (PLIP)

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain C: G.121, Y.122, H.125, G.126, L.128 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain F: R.101, K.102, L.103, A.104, D.138, K.139 Chain N: E.118, Y.124 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain G: K.104 Chain H: E.95, S.99, Y.130, V.138 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain I: Y.126, H.143, L.156, G.157, S.160 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain L: W.130, Y.165 Chain M: Y.117, G.118, R.120, F.121 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain M: Q.20, F.21, N.22, Y.24 Chain N: W.144, L.165, L.166 Ligand excluded by PLIP EDO.22: 10 residues within 4Å: Chain O: R.46, L.150, P.152, S.153, I.154, Y.155, G.165, Y.166 Chain P: M.57, T.60 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain O: F.104, Y.108, R.120 Chain W: H.95, Y.98 Ligands: EDO.34 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain U: K.104 Chain V: E.95, S.99, K.102, Y.130, V.138 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain W: G.76, Y.126 Ligands: EDO.33 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain W: Y.126, H.143, L.156, G.157, S.160 Ligands: EDO.32 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain O: R.120 Chain P: D.87 Chain W: Y.98 Ligands: EDO.23 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain Y: M.1, D.2, A.47, N.101, H.133, G.134 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain R: V.91, Q.94, S.95, L.98 Chain Y: A.62, N.63 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain 0: P.23, Y.24, F.122 Chain 1: M.140 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain 1: V.203, I.232, D.234, T.237, T.240 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain J: L.56, F.104 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain L: S.171, M.172, D.191 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.171 GOL.16: 3 residues within 4Å: Chain M: Y.58, E.222, F.235 No protein-ligand interaction detected (PLIP) GOL.25: 6 residues within 4Å: Chain Q: N.70, D.71, Q.96, L.99, D.105 Chain X: N.72 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:D.71, Q:D.105 GOL.31: 10 residues within 4Å: Chain N: Y.218, Y.219, W.252 Chain V: R.38, I.182, G.189, G.190, P.209, Y.212, E.213 5 PLIP interactions: 1 interactions with chain N, 4 interactions with chain V Hydrogen bonds: N:Y.218, V:R.38, V:G.190, V:Y.212, V:E.213 GOL.37: 2 residues within 4Å: Chain Z: G.173, D.193 1 PLIP interactions: 1 interactions with chain Z Hydrogen bonds: Z:S.192 GOL.38: 3 residues within 4Å: Chain 0: Y.117, G.118 Chain Z: Y.165 1 PLIP interactions: 1 interactions with chain 0 Hydrogen bonds: 0:Y.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Witkowska, J. et al., Crystal structure of a low molecular weight activator Blm-pep with yeast 20S proteasome - insights into the enzyme activation mechanism. Sci Rep (2017)

Release Date

2017-08-02

Peptides

Proteasome subunit alpha type-1: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-3: CQ
Proteasome subunit alpha type-4: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-6: FT
Probable proteasome subunit alpha type-7: GU
Proteasome subunit beta type-1: HV
Proteasome subunit beta type-2: IW
Proteasome subunit beta type-3: JX
Proteasome subunit beta type-4: KY
Proteasome subunit beta type-5: LZ
Proteasome subunit beta type-6: M0
Proteasome subunit beta type-7: N1
TRP-ARG-SER-TYR-TYR-ALA: 23

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
O

B
B

P
P

C
C

Q
Q

D
D

R
R

E
E

S
S

F
F

T
T

G
G

U
U

H
H

V
V

I
I

W
W

J
J

X
X

K
K

Y
Y

L
L

Z
Z

M
M

0
1

N
N

1
2

2
3

3
4

Proteasome subunit alpha type-1

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit beta type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

TRP-ARG-SER-TYR-TYR-ALA

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