SMTL ID : 5l5y.1

Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with carfilzomib

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-mer

Ligands

10 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.5: 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 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.7: 3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain K: R.19, A.164, H.165, 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.10: 3 residues within 4Å: Chain K: L.82, N.85, M.86 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:L.82 MG.12: 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: 1 interactions with chain L, 3 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166, V:S.169 MG.14: 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.21: 5 residues within 4Å: Chain Z: R.28, T.192, H.195, V.198, D.222 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198 MG.23: 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.15: 3 residues within 4Å: Chain N: T.31, R.45, Q.53 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain 1: T.31, R.45, Q.53 Ligand excluded by PLIP

6 x 3BV: N-{(2S)-2-[(morpholin-4-ylacetyl)amino]-4-phenylbutanoyl}-L-leucyl-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide(Covalent)

3BV.3: 22 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, A.27, K.33, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain I: S.5, R.99, D.125, L.126, I.127, C.129 Ligands: MES.4 15 PLIP interactions: 9 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:A.27, H:T.48, I:D.125, I:L.126, I:I.127 Hydrogen bonds: H:T.21, H:T.21, H:G.47, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125 Water bridges: H:A.50, I:L.126 3BV.8: 18 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.22, A.27, K.33, M.45, G.47, G.48, A.49, S.130, Y.169 Chain L: R.101, D.126, P.127, V.128 Ligands: MES.11 12 PLIP interactions: 10 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:A.27, K:M.45, L:V.128 Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49, L:D.126 Water bridges: K:A.50 3BV.13: 17 residues within 4Å: Chain H: H.114, H.116, S.118 Chain N: T.1, T.20, T.21, T.22, A.27, K.33, R.45, S.46, G.47, S.48, A.49, T.52, S.129, S.168 11 PLIP interactions: 11 interactions with chain N Hydrophobic interactions: N:T.22, N:A.27 Hydrogen bonds: N:T.20, N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49, N:S.129 Water bridges: N:A.50 3BV.17: 23 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, A.27, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain W: S.5, R.99, D.125, L.126, I.127, C.129 Ligands: MES.18 12 PLIP interactions: 8 interactions with chain V, 4 interactions with chain W Hydrophobic interactions: V:A.27, V:T.48, W:L.126, W:I.127 Hydrogen bonds: V:T.21, V:T.21, V:G.47, V:G.47, V:G.47, V:A.49, W:D.125, W:D.125 3BV.20: 18 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.22, A.27, K.33, M.45, G.47, G.48, A.49, S.130, Y.169 Chain Z: R.101, D.126, P.127, V.128 Ligands: MES.19 11 PLIP interactions: 9 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.27, Y:M.45, Z:V.128 Hydrogen bonds: Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:D.126 3BV.22: 16 residues within 4Å: Chain 1: T.1, T.20, T.21, T.22, A.27, K.33, R.45, S.46, G.47, S.48, A.49, S.129, S.168 Chain V: H.114, H.116, S.118 10 PLIP interactions: 10 interactions with chain 1 Hydrophobic interactions: 1:T.22, 1:A.27 Hydrogen bonds: 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:G.47, 1:A.49, 1:S.129 Water bridges: 1:A.50

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 6 residues within 4Å: Chain H: A.46, G.47, G.128, S.129 Chain Z: Y.33 Ligands: 3BV.3 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.47, H:S.129 MES.11: 12 residues within 4Å: Chain J: R.23 Chain K: T.1, G.47, S.96, M.97, G.98, Y.113, E.117, V.128, G.129, S.130 Ligands: 3BV.8 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:S.130 MES.18: 6 residues within 4Å: Chain L: Y.33 Chain V: A.46, G.47, G.128, S.129 Ligands: 3BV.17 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:S.129 MES.19: 12 residues within 4Å: Chain X: R.23 Chain Y: T.1, G.47, S.96, M.97, G.98, Y.113, E.117, V.128, G.129, S.130 Ligands: 3BV.20 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:T.1, Y:G.47, Y:S.130

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-5,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-5,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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