SMTL ID : 2zl4.1

Crystal structure of H.pylori ClpP S99A in complex with the peptide AAAA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-14-mer

Ligands

14 x ALA- ALA- ALA- ALA: Peptide substrate AAAA(Non-covalent)

ALA-ALA-ALA-ALA.1: 10 residues within 4Å: Chain A: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.72, A:I.72, A:M.100, A:L.147 Hydrogen bonds: A:G.70, A:I.72, A:M.100, A:L.127, A:L.127 Salt bridges: A:H.124 Water bridges: B:R.120, B:R.120 ALA-ALA-ALA-ALA.2: 11 residues within 4Å: Chain B: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Water bridges: C:R.120, C:R.120 Hydrophobic interactions: B:A.99, B:L.147 Hydrogen bonds: B:G.70, B:I.72, B:M.100, B:L.127, B:L.127 Salt bridges: B:H.124 ALA-ALA-ALA-ALA.3: 11 residues within 4Å: Chain C: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.72, C:I.72, C:L.147 Hydrogen bonds: C:G.70, C:G.70, C:I.72, C:M.100, C:L.127, C:L.127 Salt bridges: C:H.124 Water bridges: D:R.120 ALA-ALA-ALA-ALA.4: 11 residues within 4Å: Chain D: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.99, D:L.147 Hydrogen bonds: D:G.70, D:I.72, D:M.100, D:L.127, D:L.127 Salt bridges: D:H.124 ALA-ALA-ALA-ALA.5: 11 residues within 4Å: Chain E: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147 Chain F: R.120 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.72, E:A.99, E:M.100, E:L.147 Hydrogen bonds: E:G.70, E:G.70, E:I.72, E:M.100, E:L.127, E:L.127 Salt bridges: E:H.124 ALA-ALA-ALA-ALA.6: 11 residues within 4Å: Chain F: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, I.144, L.147 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:I.72, F:I.144, F:L.147 Hydrogen bonds: F:G.70, F:G.70, F:I.72, F:M.100, F:L.127, F:L.127 Salt bridges: F:H.124 Water bridges: G:R.120 ALA-ALA-ALA-ALA.7: 10 residues within 4Å: Chain G: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, M.151 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:V.71, G:I.72, G:A.99 Hydrogen bonds: G:G.70, G:I.72, G:M.100, G:L.127, G:L.127 Water bridges: G:T.73, A:R.120 Salt bridges: G:H.124 ALA-ALA-ALA-ALA.8: 11 residues within 4Å: Chain H: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:V.71, H:I.72, H:L.147 Hydrogen bonds: H:G.70, H:G.70, H:I.72, H:M.100, H:L.127, H:L.127 Salt bridges: H:H.124 ALA-ALA-ALA-ALA.9: 12 residues within 4Å: Chain H: R.120 Chain I: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 13 PLIP interactions: 11 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:I.72, I:I.72, I:L.147 Hydrogen bonds: I:G.70, I:G.70, I:G.70, I:I.72, I:M.100, I:L.127, I:L.127 Salt bridges: I:H.124 Water bridges: H:R.120, H:R.120 ALA-ALA-ALA-ALA.10: 10 residues within 4Å: Chain J: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:I.72, J:I.72, J:A.99, J:M.100, J:L.147 Hydrogen bonds: J:G.70, J:I.72, J:M.100, J:L.127, J:L.127 Water bridges: J:T.73 Salt bridges: J:H.124 ALA-ALA-ALA-ALA.11: 11 residues within 4Å: Chain K: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, I.144, L.147 15 PLIP interactions: 15 interactions with chain K Hydrophobic interactions: K:V.71, K:I.72, K:M.100, K:I.144, K:L.147 Hydrogen bonds: K:G.70, K:G.70, K:G.70, K:I.72, K:M.100, K:L.127, K:L.127 Water bridges: K:T.73, K:G.129 Salt bridges: K:H.124 ALA-ALA-ALA-ALA.12: 11 residues within 4Å: Chain L: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:I.72, L:I.72, L:M.100, L:L.147 Hydrogen bonds: L:G.70, L:G.70, L:G.70, L:I.72, L:M.100, L:L.127, L:L.127 Salt bridges: L:H.124 Water bridges: K:R.120 ALA-ALA-ALA-ALA.13: 11 residues within 4Å: Chain M: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 12 PLIP interactions: 11 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: M:V.71, M:I.72, M:L.147 Hydrogen bonds: M:G.70, M:G.70, M:G.70, M:I.72, M:M.100, M:L.127, M:L.127 Salt bridges: M:H.124 Water bridges: L:R.120 ALA-ALA-ALA-ALA.14: 11 residues within 4Å: Chain N: G.69, G.70, V.71, I.72, A.99, M.100, H.124, P.126, L.127, L.147, M.151 11 PLIP interactions: 11 interactions with chain N Hydrophobic interactions: N:A.99, N:L.147 Hydrogen bonds: N:G.70, N:G.70, N:G.70, N:I.72, N:M.100, N:L.127, N:L.127 Water bridges: N:T.73 Salt bridges: N:H.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, D.Y. et al., The structural basis for the activation and peptide recognition of bacterial ClpP. J.Mol.Biol. (2008)

Release Date

2008-04-22

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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