SMTL ID : 5lf4.1

Human 20S proteasome complex with Delanzomib at 2.0 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

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

Ligands

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

CL.1: 4 residues within 4Å: Chain A: Y.6, S.7, F.8 Chain C: R.5 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: R.219, R.220 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: H.88, R.91 Chain G: K.116 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: T.69 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: N.69, E.70, Q.95 Ligands: CL.6 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: N.69, L.98, P.104 Ligands: CL.5 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: V.26, I.161, G.162 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: R.86, L.114, R.117 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain D: I.31, I.170, G.171, S.174 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: T.161 Chain E: L.77, T.78 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain E: V.29, K.30, C.148, I.161, G.162, S.165 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain E: C.148, S.150, N.152 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain E: G.32, S.33, K.62, A.75, G.76 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain F: V.31, I.166, G.167, R.170 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain G: K.102, Y.103 Chain N: Y.61 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain G: K.186, F.191, E.192, Q.193, T.197 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain H: T.1, G.128, S.129 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain H: N.80, R.81 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain I: R.66, R.70 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain K: S.18, T.30, K.32, N.175 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain K: Y.66, R.69 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain J: K.29 Chain K: I.121, S.122 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain M: F.36, R.37, N.38, I.39 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain M: Y.30, R.35 Chain N: P.115, M.116 Ligands: CL.40 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain M: M.43, R.44 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain M: R.35 Chain N: S.46, G.97, G.128, G.129 Ligands: CL.38 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain N: R.19, R.29, G.171, G.172 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain O: Y.6, S.7, F.8 Chain Q: R.5 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain O: Y.101 Chain W: R.70, M.90 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain O: R.219, R.220 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain O: H.88, R.91 Chain U: K.116 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain P: N.69, E.70, Q.95 Chain W: N.72 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain Q: R.95, E.99, D.100 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain Q: V.26, I.161, G.162 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain R: I.31, I.170, G.171, S.174 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain R: S.159, T.161 Chain S: L.77, T.78 Ligand excluded by PLIP CL.56: 6 residues within 4Å: Chain S: V.29, K.30, C.148, I.161, G.162, S.165 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain S: C.148, S.150, N.152, F.154 Ligand excluded by PLIP CL.58: 5 residues within 4Å: Chain S: G.32, S.33, K.62, A.75, G.76 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain 1: Y.61 Chain U: K.102, Y.103 Ligand excluded by PLIP CL.63: 3 residues within 4Å: Chain V: T.1, G.128, S.129 Ligand excluded by PLIP CL.64: 3 residues within 4Å: Chain V: V.77, N.80, R.81 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain W: R.66, R.70 Ligand excluded by PLIP CL.69: 4 residues within 4Å: Chain Y: Q.62, I.65, Y.66, R.69 Ligand excluded by PLIP CL.70: 4 residues within 4Å: Chain Y: S.18, T.30, K.32, N.175 Ligand excluded by PLIP CL.71: 3 residues within 4Å: Chain X: K.29 Chain Y: I.121, S.122 Ligand excluded by PLIP CL.72: 2 residues within 4Å: Chain Y: D.154, L.155 Ligand excluded by PLIP CL.76: 4 residues within 4Å: Chain 0: F.36, R.37, N.38, I.39 Ligand excluded by PLIP CL.77: 6 residues within 4Å: Chain 0: R.35 Chain 1: S.46, G.97, G.128, G.129 Ligands: CL.78 Ligand excluded by PLIP CL.78: 5 residues within 4Å: Chain 0: Y.30, R.35 Chain 1: P.115, M.116 Ligands: CL.77 Ligand excluded by PLIP CL.79: 2 residues within 4Å: Chain 0: M.43, R.44 Ligand excluded by PLIP CL.80: 5 residues within 4Å: Chain 1: R.19, I.26, R.29, G.171, G.172 Ligand excluded by PLIP

8 x K: POTASSIUM ION(Non-covalent)

K.17: 4 residues within 4Å: Chain G: T.14, Y.125, N.128, 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.33 K.35: 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.60 K.44: 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.69, H2O.74 K.45: 4 residues within 4Å: Chain N: T.31, R.45, Q.53 Ligands: 6V7.46 No protein-ligand interaction detected (PLIP) K.61: 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.102 K.75: 4 residues within 4Å: Chain Z: A.183, D.186, V.187, 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.127 K.81: 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.139, H2O.142 K.82: 4 residues within 4Å: Chain 1: T.31, R.45, Q.53 Ligands: 6V7.83 No protein-ligand interaction detected (PLIP)

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.18: 3 residues within 4Å: Chain H: Q.91 Chain N: D.51, D.93 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain H: R.19, 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.40 MG.23: 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.44, H2O.45 MG.26: 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.122 MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 6 residues within 4Å: Chain K: R.19, T.164, D.167, A.168, S.170 Chain W: D.205 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: K:T.164, K:D.167, K:S.170, W:D.205, H2O.112 MG.36: 5 residues within 4Å: Chain L: D.213 Chain V: R.19, I.163, D.166, S.169 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: L:D.213, V:I.163, V:D.166, V:S.169, H2O.108 MG.62: 3 residues within 4Å: Chain 1: D.51, D.93 Chain V: Q.91 No protein-ligand interaction detected (PLIP) MG.65: 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.111, H2O.112 MG.68: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

1PE.22: 6 residues within 4Å: Chain H: L.58, M.86, Y.90, I.94 Chain I: Y.96, E.97 1 PLIP interactions: 1 interactions with chain I Water bridges: I:Y.96 1PE.25: 4 residues within 4Å: Chain I: E.97, K.98, Y.103 Chain J: D.90 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:E.97, I:K.98 Water bridges: I:R.70, I:Y.103 1PE.33: 5 residues within 4Å: Chain D: F.101 Chain K: F.54, Y.90 Chain L: S.98, F.101 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.98 1PE.34: 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 1 Water bridges: 1:S.24 1PE.42: 10 residues within 4Å: Chain G: Y.103 Chain H: F.88, R.89, Q.91 Chain N: A.54, V.55, A.58, M.86, Y.90, L.94 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.89 1PE.43: 6 residues within 4Å: Chain 0: Y.141, Y.144 Chain H: S.129 Chain N: T.22, Y.25 Chain Z: F.33 No protein-ligand interaction detected (PLIP) 1PE.60: 11 residues within 4Å: Chain 1: A.54, V.55, A.58, Y.61, M.86, Y.90, L.94 Chain U: Y.103 Chain V: F.88, R.89, Q.91 4 PLIP interactions: 1 interactions with chain U, 2 interactions with chain V, 1 interactions with chain 1 Water bridges: U:Y.103, 1:A.58 Hydrogen bonds: V:R.89, V:Q.91 1PE.67: 5 residues within 4Å: Chain W: R.66, E.97, K.98, Y.103 Chain X: D.90 6 PLIP interactions: 5 interactions with chain W, 1 interactions with chain X Hydrogen bonds: W:K.98, W:Y.103, X:D.90 Water bridges: W:R.70, W:F.100, W:G.101 1PE.73: 5 residues within 4Å: Chain Y: F.54, Y.90 Chain Z: Y.97, S.98, F.101 1 PLIP interactions: 1 interactions with chain R Water bridges: R:T.102

4 x 6V7: [(1~{R})-3-methyl-1-[[(2~{S},3~{S})-3-oxidanyl-2-[(6-phenylpyridin-2-yl)carbonylamino]butanoyl]amino]butyl]boronic acid(Covalent)

6V7.32: 14 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.22, K.33, M.45, A.46, G.47, G.48, A.49, Y.169 Chain L: D.125, P.126 15 PLIP interactions: 13 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:A.20, K:A.22, K:M.45, K:A.49, L:P.126 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.125 Water bridges: K:A.50, K:S.130 6V7.46: 17 residues within 4Å: Chain H: Y.114, H.116, S.118 Chain N: T.1, R.19, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52, S.169 Ligands: K.45 14 PLIP interactions: 13 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:T.20, N:T.22 Hydrogen bonds: N:T.1, N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49 Water bridges: N:T.1, N:A.50, N:S.130, N:S.130 pi-Stacking: H:Y.114 6V7.74: 14 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.22, K.33, M.45, A.46, G.47, G.48, A.49, Y.169 Chain Z: D.125, P.126 15 PLIP interactions: 1 interactions with chain Z, 14 interactions with chain Y Hydrophobic interactions: Z:P.126, Y:A.20, Y:A.22, Y:M.45, Y:A.49 Hydrogen bonds: Y:T.1, Y:T.21, Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49 Water bridges: Y:A.50, Y:S.130 6V7.83: 17 residues within 4Å: Chain 1: T.1, R.19, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52, S.169 Chain V: Y.114, H.116, S.118 Ligands: K.82 13 PLIP interactions: 12 interactions with chain 1, 1 interactions with chain V Hydrophobic interactions: 1:T.20, 1:R.45 Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:G.47, 1:A.49 Water bridges: 1:A.50, 1:S.130, 1:S.130 pi-Stacking: V:Y.114

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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