SMTL ID : 3krd.1

Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with Fellutamide B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-14-14-mer

Ligands

14 x ASN- GLN- LEU: Fellutamide B(Non-covalent)

ASN-GLN-LEU.1: 16 residues within 4Å: Chain C: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, A.46, G.47, T.48, A.49, A.52 Chain H: D.124 Ligands: HXD.15 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:V.31, C:A.49, C:A.52 Hydrogen bonds: C:S.20, C:S.20, C:T.21, C:T.21, C:Q.22, C:S.27, C:G.47, C:G.47, C:G.47, C:T.48, C:A.49, H:D.124 Water bridges: C:T.1, C:T.1, C:T.1, C:T.48, C:A.50, C:L.99 ASN-GLN-LEU.2: 14 residues within 4Å: Chain E: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Chain R: D.124 Ligands: HXD.16 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain R Hydrophobic interactions: E:V.31, E:A.49, E:A.52 Hydrogen bonds: E:S.20, E:S.20, E:T.21, E:T.21, E:S.27, E:G.47, E:G.47, E:G.47, E:T.48, E:A.49, R:D.124, R:D.124 Water bridges: E:T.48, E:L.99, R:D.124 ASN-GLN-LEU.3: 15 residues within 4Å: Chain G: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Chain N: D.124 Ligands: HXD.17 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:V.31, G:A.49, G:A.52 Hydrogen bonds: G:T.1, G:S.20, G:S.20, G:T.21, G:T.21, G:Q.22, G:S.27, G:G.47, G:G.47, G:T.48, G:A.49 Water bridges: G:T.1, G:T.48, G:T.48 ASN-GLN-LEU.4: 14 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Chain P: D.124 Ligands: HXD.18 17 PLIP interactions: 16 interactions with chain H, 1 interactions with chain P Hydrophobic interactions: H:V.31, H:A.49, H:A.52 Hydrogen bonds: H:S.20, H:S.20, H:T.21, H:T.21, H:Q.22, H:S.27, H:G.47, H:G.47, H:G.47, H:T.48, H:A.49, P:D.124 Water bridges: H:T.48, H:A.50 ASN-GLN-LEU.5: 15 residues within 4Å: Chain C: D.124 Chain J: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Ligands: HXD.19 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: J:V.31, J:A.49, J:A.52 Hydrogen bonds: J:T.1, J:S.20, J:S.20, J:T.21, J:T.21, J:Q.22, J:S.27, J:G.47, J:G.47, J:T.48, J:A.49 Water bridges: J:T.48, J:T.48, C:D.124 ASN-GLN-LEU.6: 15 residues within 4Å: Chain E: D.124 Chain L: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, A.46, G.47, T.48, A.49, A.52 Ligands: HXD.20 17 PLIP interactions: 16 interactions with chain L, 1 interactions with chain E Hydrophobic interactions: L:V.31, L:A.49, L:A.52 Hydrogen bonds: L:S.20, L:S.20, L:T.21, L:T.21, L:Q.22, L:S.27, L:G.47, L:G.47, L:G.47, L:T.48, L:A.49, E:D.124 Water bridges: L:T.48, L:T.48 ASN-GLN-LEU.7: 14 residues within 4Å: Chain L: D.124 Chain N: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Ligands: HXD.21 20 PLIP interactions: 20 interactions with chain N Hydrophobic interactions: N:V.31, N:A.49, N:A.52 Hydrogen bonds: N:T.1, N:T.1, N:S.20, N:S.20, N:T.21, N:T.21, N:Q.22, N:S.27, N:G.47, N:T.48, N:T.48, N:A.49 Water bridges: N:T.48, N:A.50, N:L.99, N:S.141, N:S.141 ASN-GLN-LEU.8: 13 residues within 4Å: Chain P: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, G.47, T.48, A.49, A.52 Chain V: D.124 Ligands: HXD.22 18 PLIP interactions: 16 interactions with chain P, 2 interactions with chain V Hydrophobic interactions: P:V.31, P:A.49, P:A.52 Hydrogen bonds: P:S.20, P:S.20, P:T.21, P:T.21, P:S.27, P:G.47, P:G.47, P:G.47, P:T.48, P:A.49, V:D.124, V:D.124 Water bridges: P:T.1, P:T.48, P:A.50 ASN-GLN-LEU.9: 13 residues within 4Å: Chain R: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, G.47, T.48, A.49, A.52 Chain Z: D.124 Ligands: HXD.23 18 PLIP interactions: 17 interactions with chain R, 1 interactions with chain Z Hydrophobic interactions: R:V.31, R:A.49, R:A.52 Hydrogen bonds: R:S.20, R:S.20, R:T.21, R:T.21, R:S.27, R:G.47, R:G.47, R:G.47, R:T.48, R:A.49, Z:D.124 Water bridges: R:T.1, R:T.48, R:A.50, R:L.99 ASN-GLN-LEU.10: 14 residues within 4Å: Chain J: D.124 Chain T: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Ligands: HXD.24 18 PLIP interactions: 17 interactions with chain T, 1 interactions with chain J Hydrophobic interactions: T:V.31, T:A.49, T:A.52 Hydrogen bonds: T:T.1, T:T.1, T:S.20, T:S.20, T:T.21, T:T.21, T:S.27, T:G.47, T:T.48, T:A.49, J:D.124 Water bridges: T:T.48, T:T.48, T:A.50, T:S.141 ASN-GLN-LEU.11: 14 residues within 4Å: Chain 1: D.124 Chain V: T.1, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Ligands: HXD.25 17 PLIP interactions: 15 interactions with chain V, 2 interactions with chain 1 Hydrophobic interactions: V:V.31, V:A.49, V:A.52 Hydrogen bonds: V:S.20, V:S.20, V:T.21, V:T.21, V:S.27, V:G.47, V:G.47, V:G.47, V:T.48, V:A.49, 1:D.124, 1:D.124 Water bridges: V:T.48, V:A.50 ASN-GLN-LEU.12: 15 residues within 4Å: Chain G: D.124 Chain X: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Ligands: HXD.26 17 PLIP interactions: 16 interactions with chain X, 1 interactions with chain G Hydrophobic interactions: X:V.31, X:A.49, X:A.52 Hydrogen bonds: X:T.1, X:S.20, X:S.20, X:T.21, X:T.21, X:Q.22, X:S.27, X:G.47, X:G.47, X:T.48, X:A.49 Water bridges: X:T.48, X:A.50, G:D.124 ASN-GLN-LEU.13: 15 residues within 4Å: Chain X: D.124 Chain Z: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52 Ligands: HXD.27 19 PLIP interactions: 17 interactions with chain Z, 2 interactions with chain X Hydrophobic interactions: Z:V.31, Z:A.49, Z:A.52 Hydrogen bonds: Z:T.1, Z:S.20, Z:S.20, Z:T.21, Z:T.21, Z:Q.22, Z:S.27, Z:G.47, Z:G.47, Z:T.48, Z:A.49, X:D.124 Water bridges: Z:T.48, Z:T.48, Z:A.50, X:D.124 ASN-GLN-LEU.14: 16 residues within 4Å: Chain 1: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, A.46, G.47, T.48, A.49, A.52 Chain T: D.124 Ligands: HXD.28 18 PLIP interactions: 16 interactions with chain 1, 2 interactions with chain T Hydrophobic interactions: 1:V.31, 1:A.49, 1:A.52 Hydrogen bonds: 1:S.20, 1:S.20, 1:T.21, 1:T.21, 1:S.27, 1:G.47, 1:G.47, 1:G.47, 1:T.48, 1:T.48, 1:A.49, T:D.124, T:D.124 Water bridges: 1:T.48, 1:A.50

14 x HXD: (3R)-3-HYDROXYDODECANOIC ACID(Non-covalent)

HXD.15: 6 residues within 4Å: Chain C: Q.22 Chain H: D.124, A.125, A.126 Ligands: ASN-GLN-LEU.1, ASN-GLN-LEU.1 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:Q.22 Hydrophobic interactions: H:A.125, H:A.126 HXD.16: 6 residues within 4Å: Chain E: Q.22 Chain R: D.124, A.125, A.126 Ligands: ASN-GLN-LEU.2, ASN-GLN-LEU.2 3 PLIP interactions: 3 interactions with chain R Hydrophobic interactions: R:D.124, R:A.125, R:A.126 HXD.17: 6 residues within 4Å: Chain G: Q.22 Chain N: D.124, A.125, A.126 Ligands: ASN-GLN-LEU.3, ASN-GLN-LEU.3 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain G Hydrophobic interactions: N:D.124, N:A.125, N:A.126 Hydrogen bonds: G:Q.22 HXD.18: 6 residues within 4Å: Chain H: Q.22 Chain P: D.124, A.125, A.126 Ligands: ASN-GLN-LEU.4, ASN-GLN-LEU.4 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain P Hydrogen bonds: H:Q.22 Hydrophobic interactions: P:A.125 HXD.19: 6 residues within 4Å: Chain C: D.124, A.125, A.126 Chain J: Q.22 Ligands: ASN-GLN-LEU.5, ASN-GLN-LEU.5 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain C Hydrogen bonds: J:Q.22 Hydrophobic interactions: C:D.124, C:A.125 HXD.20: 5 residues within 4Å: Chain E: D.124, A.126 Chain L: Q.22 Ligands: ASN-GLN-LEU.6, ASN-GLN-LEU.6 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain L Hydrophobic interactions: E:D.124, E:A.126 Water bridges: L:Q.22 HXD.21: 5 residues within 4Å: Chain L: D.124, A.126 Chain N: Q.22 Ligands: ASN-GLN-LEU.7, ASN-GLN-LEU.7 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain N Hydrophobic interactions: L:D.124, L:A.126 Hydrogen bonds: N:Q.22 HXD.22: 6 residues within 4Å: Chain P: Q.22 Chain V: D.124, A.125, A.126 Ligands: ASN-GLN-LEU.8, ASN-GLN-LEU.8 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain P Hydrophobic interactions: V:D.124, V:A.125, V:A.126 Hydrogen bonds: P:Q.22 HXD.23: 5 residues within 4Å: Chain R: Q.22 Chain Z: D.124, A.126 Ligands: ASN-GLN-LEU.9, ASN-GLN-LEU.9 1 PLIP interactions: 1 interactions with chain Z Hydrophobic interactions: Z:A.126 HXD.24: 6 residues within 4Å: Chain J: D.124, A.125, A.126 Chain T: Q.22 Ligands: ASN-GLN-LEU.10, ASN-GLN-LEU.10 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain T Hydrophobic interactions: J:D.124, J:A.125, J:A.126 Hydrogen bonds: T:Q.22 HXD.25: 6 residues within 4Å: Chain 1: D.124, A.125, A.126 Chain V: Q.22 Ligands: ASN-GLN-LEU.11, ASN-GLN-LEU.11 4 PLIP interactions: 1 interactions with chain V, 3 interactions with chain 1 Hydrogen bonds: V:Q.22 Hydrophobic interactions: 1:D.124, 1:A.125, 1:A.126 HXD.26: 5 residues within 4Å: Chain G: D.124, A.126 Chain X: Q.22 Ligands: ASN-GLN-LEU.12, ASN-GLN-LEU.12 2 PLIP interactions: 1 interactions with chain X, 1 interactions with chain G Hydrogen bonds: X:Q.22 Hydrophobic interactions: G:A.126 HXD.27: 6 residues within 4Å: Chain X: D.124, A.125, A.126 Chain Z: Q.22 Ligands: ASN-GLN-LEU.13, ASN-GLN-LEU.13 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain Z Hydrophobic interactions: X:D.124, X:A.125 Hydrogen bonds: Z:Q.22 HXD.28: 6 residues within 4Å: Chain 1: Q.22 Chain T: D.124, A.125, A.126 Ligands: ASN-GLN-LEU.14, ASN-GLN-LEU.14 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain 1 Hydrophobic interactions: T:D.124, T:A.125, T:A.126 Hydrogen bonds: 1:Q.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, G. et al., Fellutamide B is a potent inhibitor of the Mycobacterium tuberculosis proteasome. Arch.Biochem.Biophys. (2010)

Release Date

2010-09-29

Peptides

Proteasome subunit alpha: ABDFIKMOQSUWY0
Proteasome subunit beta: CEGHJLNPRTVXZ1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

F
F

I
I

K
K

M
M

O
O

Q
Q

S
S

U
U

W
W

Y
Y

0
1

C
C

E
E

G
G

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

Z
Z

1
2

Proteasome subunit alpha

Proteasome subunit beta

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