SMTL ID : 4qvv.1

yCP beta5-A49V mutant in complex with bortezomib

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: 6 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134, R.135 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134 MG.4: 5 residues within 4Å: Chain I: A.175, D.176, 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.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: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.165, K:D.168, W:D.205 MG.8: 3 residues within 4Å: Chain K: I.82, N.85, L.86 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:I.82 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.14: 7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, D.166, L.167, S.169 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166 MG.16: 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: 1 interactions with chain I, 3 interactions with chain Y Metal complexes: I:D.205, Y:A.165, Y:D.168, Y:S.171

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.18: 3 residues within 4Å: Chain 1: T.31, R.45, Q.53 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 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:A.49 Hydrogen bonds: H:T.1, H:S.20, H:T.21, H:T.21, H:G.47, H:G.47, H:G.47, H:A.49, I:D.125 BO2.6: 11 residues within 4Å: Chain K: T.1, A.20, T.21, K.33, M.45, A.46, G.47, G.48, V.49, Y.170 Chain L: D.126 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:T.1, K:M.45, K:V.49 Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:V.49 BO2.9: 15 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, S.168 Ligands: CL.11 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:R.45 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 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 11 PLIP interactions: 10 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:G.47, V:G.47, V:G.47, V:A.49, W:D.125 BO2.15: 11 residues within 4Å: Chain Y: T.1, A.20, T.21, K.33, M.45, A.46, G.47, G.48, V.49, Y.170 Chain Z: D.126 11 PLIP interactions: 1 interactions with chain Z, 10 interactions with chain Y Hydrogen bonds: Z:D.126, Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:V.49 Hydrophobic interactions: Y:T.1, Y:M.45, Y:V.49 BO2.17: 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, S.168 Chain V: H.114, S.118 11 PLIP interactions: 10 interactions with chain 1, 1 interactions with chain V Hydrophobic interactions: 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, V:S.118 Water bridges: 1:A.50, 1:A.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, E.M. et al., Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and ONX 0914. Structure (2015)

Release Date

2015-02-04

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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