SMTL ID : 5dl1.1

ClpP from Staphylococcus aureus in complex with AV145

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-14-mer

Ligands

14 x 5C2: 1-(propan-2-yl)-N-{[2-(thiophen-2-yl)-1,3-oxazol-4-yl]methyl}-1H-pyrazolo[3,4-b]pyridine-5-carboxamide(Non-covalent)

5C2.1: 18 residues within 4Å: Chain A: V.71, S.98, S.101, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, T.169 Chain N: I.136 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain N Hydrophobic interactions: A:Q.124, A:L.126, A:I.143, N:I.136 Hydrogen bonds: A:Q.124, A:Q.124, A:G.127 5C2.2: 19 residues within 4Å: Chain B: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 Chain K: I.136 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.71, B:F.102, B:Q.124, B:L.126, B:I.143, B:L.154, B:T.169 Hydrogen bonds: B:Q.124, B:Q.124 5C2.3: 20 residues within 4Å: Chain C: V.71, S.98, S.101, F.102, H.123, Q.124, P.125, L.126, G.127, G.128, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 Chain J: I.136 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:V.71, C:F.102, C:Q.124, C:L.154, J:I.136 Hydrogen bonds: C:Q.124, C:Q.124 5C2.4: 20 residues within 4Å: Chain D: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 Chain I: I.136 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain I Hydrophobic interactions: D:V.71, D:I.122, D:Q.124, D:I.143, D:L.154, D:T.169, I:I.136 Hydrogen bonds: D:Q.124, D:Q.124 5C2.5: 20 residues within 4Å: Chain E: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 Chain M: I.136 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain M Hydrophobic interactions: E:V.71, E:I.122, E:Q.124, E:I.143, E:L.154, E:T.169, M:I.136 Hydrogen bonds: E:Q.124, E:Q.124 5C2.6: 20 residues within 4Å: Chain F: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 Chain L: I.136 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.71, F:I.122, F:Q.124, F:I.143, F:L.154, F:T.169 Hydrogen bonds: F:Q.124, F:Q.124 5C2.7: 20 residues within 4Å: Chain G: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 Chain H: I.136 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:V.71, G:I.122, G:Q.124, G:I.143, G:L.154, G:T.169 Hydrogen bonds: G:Q.124, G:Q.124 5C2.8: 20 residues within 4Å: Chain G: I.136 Chain H: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:V.71, H:I.122, H:Q.124, H:I.143, H:L.154, H:T.169 Hydrogen bonds: H:Q.124, H:Q.124, H:G.127 5C2.9: 20 residues within 4Å: Chain D: I.136 Chain I: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:V.71, I:I.122, I:Q.124, I:I.143, I:L.154, I:T.169 Hydrogen bonds: I:Q.124, I:Q.124, I:G.127 5C2.10: 20 residues within 4Å: Chain C: I.136 Chain J: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 10 PLIP interactions: 9 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: J:V.71, J:I.122, J:Q.124, J:I.143, J:L.154, J:T.169, C:I.136 Hydrogen bonds: J:Q.124, J:Q.124, J:G.127 5C2.11: 20 residues within 4Å: Chain B: I.136 Chain K: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.71, K:I.122, K:Q.124, K:I.143, K:L.154, K:T.169 Hydrogen bonds: K:Q.124, K:Q.124, K:G.127 5C2.12: 20 residues within 4Å: Chain F: I.136 Chain L: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 9 PLIP interactions: 8 interactions with chain L, 1 interactions with chain F Hydrophobic interactions: L:V.71, L:F.102, L:Q.124, L:L.126, L:I.143, L:L.154, F:I.136 Hydrogen bonds: L:Q.124, L:Q.124 5C2.13: 20 residues within 4Å: Chain E: I.136 Chain M: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 10 PLIP interactions: 1 interactions with chain E, 9 interactions with chain M Hydrophobic interactions: E:I.136, M:V.71, M:I.122, M:Q.124, M:I.143, M:L.154, M:T.169 Hydrogen bonds: M:Q.124, M:Q.124, M:G.127 5C2.14: 20 residues within 4Å: Chain A: I.136 Chain N: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, P.125, L.126, G.127, Q.132, H.142, I.143, T.146, R.147, L.150, N.151, L.154, T.169 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:V.71, N:I.122, N:Q.124, N:I.143, N:L.154, N:T.169 Hydrogen bonds: N:Q.124, N:Q.124, N:G.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pahl, A. et al., Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-11-25

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit

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