SMTL ID : 5c90.1

Staphylococcus aureus ClpP mutant - Y63A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-14-mer

Ligands

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 9 residues within 4Å: Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.71, A:F.102, A:L.150, A:L.154 Hydrogen bonds: A:H.123, A:H.123 MPD.2: 8 residues within 4Å: Chain B: V.71, S.98, M.99, I.122, H.123, Q.124, P.125, L.150 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.71, B:P.125, B:L.150 Hydrogen bonds: B:S.98, B:H.123, B:Q.124 MPD.3: 9 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.71, C:I.122, C:L.150 Hydrogen bonds: C:H.123 MPD.4: 8 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.71, D:F.102, D:L.150 Hydrogen bonds: D:H.123, D:H.123 MPD.5: 8 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:V.71, E:F.102, E:L.150 Hydrogen bonds: E:H.123, E:H.123 MPD.6: 9 residues within 4Å: Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:V.71, F:F.102, F:I.122, F:L.150, F:L.154 Hydrogen bonds: F:H.123, F:H.123 MPD.7: 8 residues within 4Å: Chain G: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:V.71, G:F.102, G:L.150 Hydrogen bonds: G:H.123, G:H.123 MPD.8: 8 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:V.71, H:F.102, H:L.150 Hydrogen bonds: H:H.123, H:H.123 MPD.9: 9 residues within 4Å: Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:V.71, I:F.102, I:I.122, I:L.150, I:L.154 Hydrogen bonds: I:H.123, I:H.123 MPD.10: 8 residues within 4Å: Chain J: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.71, J:F.102, J:L.150 Hydrogen bonds: J:H.123, J:H.123 Water bridges: J:M.99 MPD.11: 9 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:V.71, K:F.102, K:L.150, K:L.154 Hydrogen bonds: K:H.123, K:H.123 MPD.12: 8 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:V.71, L:I.122, L:L.150 Hydrogen bonds: L:H.123 MPD.13: 8 residues within 4Å: Chain M: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:V.71, M:F.102, M:L.150 Hydrogen bonds: M:H.123, M:H.123 MPD.14: 9 residues within 4Å: Chain N: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:V.71, N:F.102, N:L.150, N:L.154 Hydrogen bonds: N:H.123, N:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, T. et al., Characterization of Gain-of-Function Mutant Provides New Insights into ClpP Structure. Acs Chem.Biol. (2016)

Release Date

2016-05-25

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