SMTL ID : 2zl2.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-14-mer

Ligands

8 x ASN- VAL- LEU- GLY: A peptide substrate-NVLGFTQ(Non-covalent)

ASN-VAL-LEU-GLY.1: 7 residues within 4Å: Chain A: G.70, V.71, I.72, M.100, H.124, P.126, L.127 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.72 Hydrogen bonds: A:G.70, A:I.72, A:M.100, A:L.127, A:L.127 ASN-VAL-LEU-GLY.2: 15 residues within 4Å: Chain B: G.69, G.70, V.71, I.72, S.99, M.100, F.103, H.124, P.126, L.127, I.144, L.147, M.151 Chain C: R.120, Y.175 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.72, B:I.144, B:L.147 Hydrogen bonds: B:G.70, B:G.70, B:I.72, B:M.100, B:L.127, B:L.127 Salt bridges: B:H.124 pi-Cation interactions: C:R.120 ASN-VAL-LEU-GLY.3: 12 residues within 4Å: Chain C: G.70, V.71, I.72, T.73, S.99, M.100, H.124, P.126, L.127, I.144, M.151 Chain D: Q.96 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:Q.96, D:Q.96, C:G.70, C:I.72, C:L.127, C:L.127 Hydrophobic interactions: C:V.71, C:V.71, C:I.72, C:I.144 ASN-VAL-LEU-GLY.6: 8 residues within 4Å: Chain G: G.70, V.71, I.72, S.99, M.100, H.124, P.126, L.127 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:V.71, G:I.72 Hydrogen bonds: G:G.70, G:I.72, G:L.127, G:L.127 ASN-VAL-LEU-GLY.7: 14 residues within 4Å: Chain H: G.69, G.70, V.71, I.72, S.99, M.100, F.103, H.124, Q.125, P.126, L.127, L.147, M.151 Chain N: R.120 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:V.71, H:I.72, H:F.103, H:P.126, H:L.147 Hydrogen bonds: H:G.70, H:G.70, H:I.72, H:M.100, H:L.127, H:L.127 ASN-VAL-LEU-GLY.8: 9 residues within 4Å: Chain K: G.70, V.71, I.72, S.99, M.100, H.124, P.126, L.127, L.147 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.71, K:I.72, K:I.72, K:L.147 Hydrogen bonds: K:G.70, K:I.72, K:S.99, K:L.127, K:L.127 ASN-VAL-LEU-GLY.9: 9 residues within 4Å: Chain M: G.70, V.71, I.72, S.99, M.100, H.124, P.126, L.127, L.147 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:I.72, M:L.147 Hydrogen bonds: M:G.70, M:I.72, M:M.100, M:L.127, M:L.127 ASN-VAL-LEU-GLY.10: 12 residues within 4Å: Chain M: R.120 Chain N: G.70, V.71, I.72, S.99, M.100, H.124, P.126, L.127, G.128, L.147, M.151 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:I.72, N:L.147 Hydrogen bonds: N:G.70, N:I.72, N:M.100, N:L.127, N:L.127, M:R.120

2 x UNK- UNK- UNK: A peptide substrate-NVLGFTQ for Chain R and S(Non-covalent)

UNK-UNK-UNK.4: 11 residues within 4Å: Chain E: G.70, V.71, I.72, S.99, M.100, H.124, P.126, L.127, G.128, L.147, M.151 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.72, E:M.100 Hydrogen bonds: E:G.70, E:I.72, E:S.99, E:L.127, E:L.127 UNK-UNK-UNK.5: 8 residues within 4Å: Chain F: G.70, V.71, I.72, S.99, M.100, H.124, P.126, L.127 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.71, F:I.72, F:I.72, F:M.100 Hydrogen bonds: F:G.70, F:I.72, F:S.99, F:L.127, F:L.127

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

Related Entries With Identical Sequence