SMTL ID : 5l5f.1

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with bortezomib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: 5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134 MG.4: 6 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.164, D.167, A.168, S.170 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.164, Y:D.167, Y:S.170, I:D.205 MG.5: 3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain K: R.19, A.164, D.167, A.168, S.170 Chain W: D.205 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.164, K:D.167, K:S.170, W:D.205 MG.8: 7 residues within 4Å: Chain L: D.222 Chain V: R.19, G.162, I.163, D.166, L.167, S.169 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, V:S.169, L:D.222 MG.10: 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.15: 5 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198 4 PLIP interactions: 3 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: Z:T.192, Z:H.195, Z:V.198, H2O.30 MG.18: 5 residues within 4Å: Chain 1: R.19, I.163, D.166, S.169 Chain M: L.47 3 PLIP interactions: 3 interactions with chain 1 Metal complexes: 1:I.163, 1:D.166, 1:S.169

4 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.11: 4 residues within 4Å: Chain N: T.31, R.45, Q.53 Ligands: BO2.9 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain 1: T.31, R.45, Q.53 Ligands: BO2.16 Ligand excluded by PLIP

6 x BO2: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE(Covalent)

BO2.3: 14 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52 Chain I: D.125, C.129 12 PLIP interactions: 11 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:T.1, H:A.49 Hydrogen bonds: H:T.1, H:S.20, H:T.21, H:T.21, H:Q.22, H:G.47, H:G.47, H:G.47, H:A.49, I:D.125 BO2.6: 13 residues within 4Å: Chain K: T.1, A.20, S.21, S.27, V.31, K.33, M.45, S.46, G.47, C.48, A.49 Chain L: D.126, S.130 12 PLIP interactions: 11 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:V.31, K:M.45, K:A.49 Hydrogen bonds: K:T.1, K:S.21, K:S.21, K:S.27, K:G.47, K:G.47, K:G.47, K:A.49, L:S.130 BO2.9: 14 residues within 4Å: Chain H: H.114, S.118 Chain N: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52 Ligands: CL.11 11 PLIP interactions: 9 interactions with chain N, 2 interactions with chain H Hydrogen bonds: N:T.1, N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49, H:S.118 Water bridges: N:A.50, N:A.50 pi-Stacking: H:H.114 BO2.13: 14 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52 Chain W: D.125, C.129 12 PLIP interactions: 11 interactions with chain V, 1 interactions with chain W Hydrophobic interactions: V:T.1, V:A.49 Hydrogen bonds: V:T.1, V:S.20, V:T.21, V:T.21, V:Q.22, V:G.47, V:G.47, V:G.47, V:A.49, W:D.125 BO2.14: 12 residues within 4Å: Chain Y: T.1, A.20, S.21, S.27, K.33, M.45, S.46, G.47, C.48, A.49 Chain Z: D.126, S.130 11 PLIP interactions: 10 interactions with chain Y, 1 interactions with chain Z Hydrophobic interactions: Y:M.45, Y:A.49 Hydrogen bonds: Y:T.1, Y:S.21, Y:S.21, Y:S.27, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:S.130 BO2.16: 14 residues within 4Å: Chain 1: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52 Chain V: H.114, S.118 Ligands: CL.17 11 PLIP interactions: 9 interactions with chain 1, 2 interactions with chain V Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:G.47, 1:A.49, V:S.118 Water bridges: 1:A.50, 1:S.129 pi-Stacking: V:H.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, E.M. et al., A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i. EMBO J. (2016)

Release Date

2016-11-09

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-8,Proteasome subunit beta type-5: KY
Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,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

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 alpha type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-8,Proteasome subunit beta type-5

Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-1

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