SMTL ID : 5cz5.1

Yeast 20S proteasome beta1-T1A mutant in complex with Carfilzomib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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.2: 2 residues within 4Å: Chain G: F.73, C.74 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain I: A.175, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.175, I:D.178, I:S.181 MG.7: 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.9: 6 residues within 4Å: Chain K: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.165, K:D.168, K:S.171, W:D.205 MG.11: 7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, 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.12: 6 residues within 4Å: Chain 0: L.47 Chain N: R.29, I.173, D.176, G.177, S.179 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:I.173, N:D.176, N:S.179 MG.19: 5 residues within 4Å: Chain Z: R.28, T.192, H.195, V.198, D.222 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.192, Z:V.198

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

CL.3: 3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain N: L.9, T.41, R.55, A.59, Q.63 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain 1: L.9, T.41, R.55, Q.63 Ligand excluded by PLIP

4 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.4: 19 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, A.27, K.33, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain I: R.99, D.125, L.126, I.127, C.129 Ligands: MES.5 14 PLIP interactions: 10 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:A.27, H:K.33, H:T.48, 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 3BV.8: 19 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, Y.170 Chain L: R.101, H.108, D.126, P.127, V.128, S.130 Ligands: MES.10 13 PLIP interactions: 3 interactions with chain L, 10 interactions with chain K Hydrophobic interactions: L:V.128, L:V.128, K:A.20, K:A.27, K:A.49 Hydrogen bonds: L:D.126, K:T.1, K:T.21, K:T.21, K:G.47, K:G.47, K:A.49 Water bridges: K:A.50 3BV.15: 18 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, A.27, C.31, K.33, G.47, T.48, A.49, T.52, G.168 Chain W: S.5, R.99, D.125, L.126 Ligands: MES.16 13 PLIP interactions: 4 interactions with chain W, 9 interactions with chain V Hydrophobic interactions: W:D.125, W:L.126, V:A.27, V:K.33, V:T.48 Hydrogen bonds: W:D.125, W:D.125, V:T.21, V:T.21, V:G.47, V:G.47, V:G.47, V:A.49 3BV.17: 18 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.22, A.27, K.33, G.47, G.48, A.49, Y.170 Chain Z: R.101, H.108, D.126, P.127, V.128, S.130 Ligands: MES.18 11 PLIP interactions: 9 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.20, Y:A.27, 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

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

MES.5: 5 residues within 4Å: Chain H: G.47, G.128, S.129 Chain Z: Y.33 Ligands: 3BV.4 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.47 MES.10: 9 residues within 4Å: Chain K: T.1, G.47, S.96, M.97, G.98, S.117, G.130, S.131 Ligands: 3BV.8 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:G.47, K:S.131 MES.16: 6 residues within 4Å: Chain L: Y.33 Chain V: T.1, G.47, G.128, S.129 Ligands: 3BV.15 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:T.1, V:S.129 MES.18: 9 residues within 4Å: Chain Y: T.1, G.47, S.96, M.97, G.98, S.117, G.130, S.131 Ligands: 3BV.17 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:T.1, Y:G.47, Y:S.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, E.M. et al., A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Nat Commun (2016)

Release Date

2016-03-23

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

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-6

Proteasome subunit beta type-7

Proteasome subunit beta type-1

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