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SMTL ID : 6zp8.1

Yeast 20S proteasome in complex with glidobactin-like natural product HB335

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-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1:	6 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134, R.135 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134
MG.4:	4 residues within 4Å: Chain I: A.175, D.178, S.181, D.205 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.178, I:S.181
MG.6:	6 residues within 4Å: Chain K: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 3 PLIP interactions: 1 interactions with chain W, 2 interactions with chain K Metal complexes: W:D.205, K:A.165, K:D.168
MG.7:	5 residues within 4Å: Chain 0: L.47 Chain N: R.19, I.163, D.166, S.169 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:I.163, N:D.166, N:S.169
MG.10:	6 residues within 4Å: Chain L: D.222 Chain V: I.163, W.164, D.166, L.167, S.169 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166
MG.11:	4 residues within 4Å: Chain W: A.175, D.178, S.181, D.205 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.178, W:S.181
MG.13:	7 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, D.168, A.169, S.171 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:D.168, Y:S.171, I:D.205
MG.14:	6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:V.198

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

CL.2:	3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP
CL.8:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

4 x QOE: (2~{S},3~{R})-~{N}-[(5~{S},8~{S},10~{S})-5-methyl-10-oxidanyl-2,7-bis(oxidanylidene)-1,6-diazacyclododec-8-yl]-3-oxidanyl-2-(3-phenylpropanoylamino)butanamide(Covalent)

QOE.3:	11 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, K.33, G.47, T.48, A.49 Chain I: R.99, D.125, L.126 10 PLIP interactions: 4 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: I:L.126, H:T.1 Hydrogen bonds: I:D.125, I:D.125, I:D.125, H:T.21, H:T.21, H:G.47, H:G.47, H:A.49
QOE.5:	9 residues within 4Å: Chain K: T.1, A.20, T.21, K.33, G.47, A.49 Chain L: D.126, P.127, S.130 10 PLIP interactions: 6 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:T.1, L:P.127, L:P.127 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:A.49, L:D.126, L:S.130
QOE.9:	12 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, K.33, G.45, G.47, T.48, A.49 Chain W: R.99, D.125, L.126 12 PLIP interactions: 5 interactions with chain W, 7 interactions with chain V Hydrophobic interactions: W:L.126, V:T.1 Hydrogen bonds: W:D.125, W:D.125, W:D.125, V:T.1, V:T.21, V:T.21, V:G.47, V:G.47, V:A.49 Water bridges: W:D.125
QOE.12:	10 residues within 4Å: Chain Y: T.1, A.20, T.21, K.33, M.45, G.47, A.49 Chain Z: D.126, P.127, S.130 11 PLIP interactions: 6 interactions with chain Y, 5 interactions with chain Z Hydrophobic interactions: Y:T.1, Z:D.126, Z:P.127, Z:P.127 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49, Z:D.126, Z:S.130

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Zhao, L. et al., Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-like Proteasome Inhibitors from Photorhabdus laumondii. Chembiochem (2021)

Release Date

2021-05-19

Peptides

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

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
a

N
N

1
b

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Proteasome subunit alpha type-2

Toggle Identical (AO)

Proteasome subunit alpha type-3

Toggle Identical (BP)

Proteasome subunit alpha type-4

Toggle Identical (CQ)

Proteasome subunit alpha type-5

Toggle Identical (DR)

Proteasome subunit alpha type-6

Toggle Identical (ES)

Probable proteasome subunit alpha type-7

Toggle Identical (FT)

Proteasome subunit alpha type-1

Toggle Identical (GU)

Proteasome subunit beta type-2

Toggle Identical (HV)

Proteasome subunit beta type-3

Toggle Identical (IW)

Proteasome subunit beta type-4

Toggle Identical (JX)

Proteasome subunit beta type-5

Toggle Identical (KY)

Proteasome subunit beta type-6

Toggle Identical (LZ)

Proteasome subunit beta type-7

Proteasome subunit beta type-1

Toggle Identical (N1)

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Cartoon
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Background

Transparent

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