SMTL ID : 4x6z.1

Yeast 20S proteasome in complex with PR-VI modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 2 residues within 4Å: Chain A: Y.24, F.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.24 MPD.5: 4 residues within 4Å: Chain A: Y.58, F.235 Chain B: R.194, E.195 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.195, A:Y.58 Hydrogen bonds: B:E.195 MPD.47: 5 residues within 4Å: Chain M: R.23 Chain N: M.172, G.173, D.191, D.193 No protein-ligand interaction detected (PLIP) MPD.52: 2 residues within 4Å: Chain O: Y.24, F.122 2 PLIP interactions: 2 interactions with chain O Hydrophobic interactions: O:Y.24, O:F.122 MPD.59: 3 residues within 4Å: Chain O: E.237 Chain P: R.194, E.195 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:R.194 Hydrogen bonds: P:E.195 MPD.78: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.82: 7 residues within 4Å: Chain X: T.20, S.65, G.66, G.147, S.148, S.187 Ligands: MG.87 2 PLIP interactions: 2 interactions with chain X Hydrogen bonds: X:G.66, X:S.148 MPD.91: 7 residues within 4Å: Chain R: R.99, I.100 Chain Y: A.83, Q.86 Chain Z: Q.89, S.92, S.93 3 PLIP interactions: 2 interactions with chain Z, 1 interactions with chain Y Hydrogen bonds: Z:Q.89, Z:S.92 Hydrophobic interactions: Y:A.83 MPD.98: 5 residues within 4Å: Chain 1: T.76, G.122, G.205, S.206 Ligands: GOL.99 2 PLIP interactions: 2 interactions with chain 1 Hydrogen bonds: 1:T.76, 1:S.206

38 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.26, Y.125, H.127 Ligand excluded by PLIP GOL.3: 1 residues within 4Å: Chain A: R.120 Ligand excluded by PLIP GOL.6: 4 residues within 4Å: Chain B: D.80, D.234, K.235, G.238 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain B: I.38, Y.63, G.64 Chain X: L.134 Ligand excluded by PLIP GOL.13: 2 residues within 4Å: Chain C: Y.106 Chain J: Y.80 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain C: R.46, G.47, K.48, D.192, H.193 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain C: Y.108 Chain K: H.95, Y.98 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain C: F.73, K.98 Chain I: D.114 Chain J: Q.88 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain F: R.111, G.115, Y.156 Chain G: R.86, S.87 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain G: R.166, Y.167, N.168 Chain H: L.56, S.57, S.58 Ligand excluded by PLIP GOL.23: 1 residues within 4Å: Chain H: N.41 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain G: D.118, R.122 Chain H: V.83, N.86 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain H: H.69, G.217, D.219, T.220, P.221 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain H: F.99, R.101, R.107 Chain P: E.106 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain I: H.123, Y.126 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain I: R.91, E.94, E.95, S.98 Ligand excluded by PLIP GOL.30: 10 residues within 4Å: Chain J: T.20, R.38, T.39, K.52, R.64, S.65, G.66, S.67, A.68, T.71 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain J: T.39, T.41, A.46 Chain K: H.143, S.147, D.149 Ligand excluded by PLIP GOL.36: 2 residues within 4Å: Chain K: Y.126, G.157 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain D: R.99 Chain K: E.82, Q.86 Chain L: Q.89, S.92, G.128 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain M: M.1, G.48, Q.99, N.101, Y.121 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain 0: L.163, Q.166, E.167, K.170 Chain N: D.216 Ligand excluded by PLIP GOL.49: 3 residues within 4Å: Chain N: N.218, D.227, Y.230 Ligand excluded by PLIP GOL.53: 3 residues within 4Å: Chain N: Y.165 Chain O: Y.117, G.118 Ligand excluded by PLIP GOL.54: 3 residues within 4Å: Chain O: N.74, G.75, Y.125 Ligand excluded by PLIP GOL.60: 4 residues within 4Å: Chain P: D.80, Q.153, D.234, G.238 Ligand excluded by PLIP GOL.61: 2 residues within 4Å: Chain P: Y.63, G.64 Ligand excluded by PLIP GOL.66: 2 residues within 4Å: Chain Q: Y.108 Chain Y: H.95 Ligand excluded by PLIP GOL.67: 5 residues within 4Å: Chain Q: F.73, R.91, K.98 Chain W: D.114 Chain X: Q.88 Ligand excluded by PLIP GOL.75: 4 residues within 4Å: Chain U: R.166, N.168 Chain V: S.57, S.58 Ligand excluded by PLIP GOL.79: 6 residues within 4Å: Chain V: H.69, K.102, Y.137, G.217, D.219, P.221 Ligand excluded by PLIP GOL.83: 2 residues within 4Å: Chain B: Q.35 Chain X: D.110 Ligand excluded by PLIP GOL.84: 8 residues within 4Å: Chain X: T.39, T.50, R.64, S.65, G.66, A.68, T.71, Q.72 Ligand excluded by PLIP GOL.89: 3 residues within 4Å: Chain Y: G.76, Y.126, G.157 Ligand excluded by PLIP GOL.92: 1 residues within 4Å: Chain Z: L.56 Ligand excluded by PLIP GOL.99: 5 residues within 4Å: Chain 1: S.171, M.172, D.191, D.193 Ligands: MPD.98 Ligand excluded by PLIP GOL.100: 3 residues within 4Å: Chain 1: Y.165 Chain A: Y.117, F.121 Ligand excluded by PLIP GOL.101: 5 residues within 4Å: Chain 1: N.218, D.227, Y.230, L.231 Chain M: H.146 Ligand excluded by PLIP

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

MG.4: 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.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: D.193 Chain K: W.193 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: K.251, D.253, F.254 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: Q.135 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain D: G.223 No protein-ligand interaction detected (PLIP) MG.18: 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.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain H: E.27 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain J: T.20, G.66, S.148 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain J: L.134 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain K: C.60, A.61 Chain L: I.130, E.132 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.132 MG.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain L: E.97, F.100 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain L: F.104 No protein-ligand interaction detected (PLIP) MG.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Chain L: Y.103 No protein-ligand interaction detected (PLIP) MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain N: T.76, S.206 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain N: Q.137 No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Chain O: Y.125 No protein-ligand interaction detected (PLIP) MG.56: 1 residues within 4Å: Chain O: D.136 No protein-ligand interaction detected (PLIP) MG.57: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.58: 1 residues within 4Å: Chain O: N.22 No protein-ligand interaction detected (PLIP) MG.62: 1 residues within 4Å: Chain P: E.73 No protein-ligand interaction detected (PLIP) MG.63: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.64: 1 residues within 4Å: Chain I: R.72 No protein-ligand interaction detected (PLIP) MG.65: 1 residues within 4Å: Chain H: Y.94 No protein-ligand interaction detected (PLIP) MG.68: 1 residues within 4Å: Chain Q: E.242 No protein-ligand interaction detected (PLIP) MG.69: 1 residues within 4Å: Chain R: L.250 No protein-ligand interaction detected (PLIP) MG.70: 2 residues within 4Å: Chain S: N.97, Y.98 No protein-ligand interaction detected (PLIP) MG.71: 1 residues within 4Å: Chain S: T.90 No protein-ligand interaction detected (PLIP) MG.72: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.73: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.74: 2 residues within 4Å: Chain T: E.189, Q.231 No protein-ligand interaction detected (PLIP) MG.76: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.77: 2 residues within 4Å: Chain U: K.194, K.235 No protein-ligand interaction detected (PLIP) MG.80: 1 residues within 4Å: Chain V: D.209 No protein-ligand interaction detected (PLIP) MG.81: 2 residues within 4Å: Chain V: Q.90, N.93 No protein-ligand interaction detected (PLIP) MG.85: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.86: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.87: 2 residues within 4Å: Chain X: L.134 Ligands: MPD.82 No protein-ligand interaction detected (PLIP) MG.88: 2 residues within 4Å: Chain X: L.112, T.113 No protein-ligand interaction detected (PLIP) MG.90: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.93: 3 residues within 4Å: Chain 0: V.126, E.127 Chain Z: K.39 No protein-ligand interaction detected (PLIP) MG.94: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.95: 1 residues within 4Å: Chain Y: Y.119 No protein-ligand interaction detected (PLIP) MG.96: 1 residues within 4Å: Chain 0: M.174 No protein-ligand interaction detected (PLIP) MG.97: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.102: 2 residues within 4Å: Chain 1: Q.137 Chain U: T.98 No protein-ligand interaction detected (PLIP) MG.103: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Witkowska, J. et al., Crystal structures revealed the common place of binding of low-molecularmass activators with the 20S proteasome. To Be Published

Release Date

2015-12-23

Peptides

Proteasome subunit beta type-6: AO
Proteasome subunit beta type-7: BP
Proteasome subunit alpha type-1: CQ
Proteasome subunit alpha type-2: DR
Proteasome subunit alpha type-3: ES
Proteasome subunit alpha type-4: FT
Proteasome subunit alpha type-5: GU
Proteasome subunit alpha type-6: HV
Probable proteasome subunit alpha type-7: IW
Proteasome subunit beta type-1: JX
Proteasome subunit beta type-2: KY
Proteasome subunit beta type-3: LZ
Proteasome subunit beta type-4: M0
Proteasome subunit beta type-5: N1
synthetic peptide (polymer): 23

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

O
M

B
2

P
N

C
A

Q
O

D
B

R
P

E
C

S
Q

F
D

T
R

G
E

U
S

H
F

V
T

I
G

W
U

J
H

X
V

K
I

Y
W

L
J

Z
X

M
K

0
Y

N
L

1
Z

2
a

3
e

Proteasome subunit beta type-6

Proteasome subunit beta type-7

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

synthetic peptide (polymer)

Related Entries With Identical Sequence