SMTL ID : 5lex.1

Native human 20S proteasome in Mg-Acetate at 2.2 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

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

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain G: T.14, Y.125, N.128, A.129, M.131 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:T.14, G:Y.125, G:N.128, G:M.131, H2O.27 K.11: 4 residues within 4Å: Chain L: A.183, D.186, V.187, T.189 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:A.183, L:D.186, L:T.189, H2O.54 K.14: 4 residues within 4Å: Chain N: R.19, M.164, D.167, S.170 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:M.164, N:D.167, N:S.170, H2O.66, H2O.68 K.15: 4 residues within 4Å: Chain U: T.14, Y.125, N.128, M.131 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:T.14, U:Y.125, U:N.128, U:M.131, H2O.92 K.21: 3 residues within 4Å: Chain Z: A.183, D.186, T.189 4 PLIP interactions: 3 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: Z:A.183, Z:D.186, Z:T.189, H2O.111 K.24: 4 residues within 4Å: Chain 1: R.19, M.164, D.167, S.170 5 PLIP interactions: 3 interactions with chain 1, 2 Ligand-Water interactions Metal complexes: 1:M.164, 1:D.167, 1:S.170, H2O.126, H2O.128

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain H: I.163, D.166, S.169 Chain Z: D.213 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: H:I.163, H:D.166, H:S.169, Z:D.213, H2O.36 MG.4: 3 residues within 4Å: Chain I: V.175, D.178, S.181 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:V.175, I:D.178, I:S.181, H2O.41, H2O.41 MG.6: 6 residues within 4Å: Chain I: D.205 Chain Y: R.19, T.164, D.167, A.168, S.170 5 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: Y:T.164, Y:D.167, Y:S.170, I:D.205, H2O.109 MG.7: 1 residues within 4Å: Chain J: P.97 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain K: R.19, T.164, D.167, A.168, S.170 Chain W: D.205 5 PLIP interactions: 1 interactions with chain W, 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: W:D.205, K:T.164, K:D.167, K:S.170, H2O.50 MG.12: 5 residues within 4Å: Chain L: D.213 Chain V: R.19, I.163, D.166, S.169 5 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: V:I.163, V:D.166, V:S.169, L:D.213, H2O.96 MG.16: 3 residues within 4Å: Chain 1: D.51, D.93 Chain V: Q.91 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain W: V.175, D.178, S.181 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:V.175, W:D.178, W:S.181, H2O.99, H2O.99 MG.19: 1 residues within 4Å: Chain X: P.97 No protein-ligand interaction detected (PLIP)

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

1PE.3: 3 residues within 4Å: Chain H: Y.90 Chain I: Y.96, E.97 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:Y.90 Water bridges: I:Y.96 1PE.5: 4 residues within 4Å: Chain I: R.66, E.97, K.98 Chain J: D.90 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.98 Water bridges: I:R.70 1PE.9: 4 residues within 4Å: Chain K: F.54, Y.90 Chain L: S.98, F.101 No protein-ligand interaction detected (PLIP) 1PE.10: 5 residues within 4Å: Chain 1: T.22 Chain L: F.33 Chain M: Y.141, Y.144 Chain V: S.129 1 PLIP interactions: 1 interactions with chain V Water bridges: V:S.129 1PE.13: 7 residues within 4Å: Chain G: Y.103 Chain H: F.88, R.89, Q.91 Chain N: A.58, Y.90, L.94 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.89 1PE.18: 4 residues within 4Å: Chain W: R.66, E.97, K.98 Chain X: D.90 3 PLIP interactions: 3 interactions with chain W Hydrogen bonds: W:K.98 Water bridges: W:F.100, W:G.101 1PE.20: 5 residues within 4Å: Chain R: N.98 Chain Y: Y.90 Chain Z: Y.97, S.98, F.101 2 PLIP interactions: 2 interactions with chain R Water bridges: R:T.102, R:T.102 1PE.22: 5 residues within 4Å: Chain 0: Y.141, Y.144 Chain H: S.129 Chain N: T.22 Chain Z: F.33 No protein-ligand interaction detected (PLIP) 1PE.23: 8 residues within 4Å: Chain 1: A.58, Y.61, Y.90, L.94 Chain U: Y.103 Chain V: F.88, R.89, Q.91 4 PLIP interactions: 1 interactions with chain 1, 2 interactions with chain V, 1 interactions with chain U Water bridges: 1:A.58, U:Y.103 Hydrogen bonds: V:R.89, V:Q.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schrader, J. et al., The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design. Science (2016)

Release Date

2016-08-17

Peptides

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

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-3

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

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