SMTL ID : 5g1s.1 (1 other biounit)

Open conformation of Francisella tularensis ClpP at 1.7 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-14-mer

Ligands

14 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.126, A:H.126 ACT.4: 6 residues within 4Å: Chain B: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.104, B:H.126, B:H.126 ACT.6: 6 residues within 4Å: Chain C: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.105, C:H.126 ACT.10: 6 residues within 4Å: Chain D: S.101, S.104, L.105, I.125, H.126, L.157 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.104, D:L.105, D:H.126, D:H.126, D:H.126 ACT.13: 6 residues within 4Å: Chain E: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.104, E:L.105, E:H.126 ACT.15: 6 residues within 4Å: Chain F: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.104, F:H.126, F:H.126 ACT.18: 6 residues within 4Å: Chain G: S.101, S.104, L.105, I.125, H.126, L.157 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:S.101, G:S.104, G:H.126, G:H.126, G:H.126 ACT.20: 6 residues within 4Å: Chain H: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:H.126, H:H.126 ACT.22: 6 residues within 4Å: Chain I: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.126, I:H.126 ACT.24: 6 residues within 4Å: Chain J: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:S.104, J:H.126, J:H.126 ACT.25: 6 residues within 4Å: Chain K: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:L.105 Hydrogen bonds: K:S.104, K:H.126, K:H.126 ACT.28: 6 residues within 4Å: Chain L: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:S.104, L:L.105, L:H.126 ACT.32: 6 residues within 4Å: Chain M: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:S.101, M:S.104, M:H.126 ACT.35: 6 residues within 4Å: Chain N: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:S.104, N:H.126, N:H.126

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

MPD.2: 5 residues within 4Å: Chain B: R.115, H.160, T.161, G.162, G.187 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.162 MPD.5: 5 residues within 4Å: Chain C: T.161, G.162, Q.163, A.185, Y.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.162 MPD.12: 7 residues within 4Å: Chain E: K.112, R.115, H.159, H.160, T.161, G.162, G.187 No protein-ligand interaction detected (PLIP) MPD.14: 5 residues within 4Å: Chain F: R.115, H.159, H.160, T.161, G.187 No protein-ligand interaction detected (PLIP) MPD.16: 5 residues within 4Å: Chain G: Y.64, Y.66, I.94, I.193, R.196 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.64, G:I.94, G:I.193 Hydrogen bonds: G:Y.66 MPD.26: 6 residues within 4Å: Chain L: Y.64, Y.66, Y.116, I.193, R.196 Chain M: F.86 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:F.86, L:Y.64, L:I.193 Hydrogen bonds: L:R.196 MPD.29: 6 residues within 4Å: Chain M: Y.64, I.94, Y.116, I.193, R.196 Chain N: F.86 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:Y.64, M:Y.116, M:I.193, N:F.86 MPD.34: 7 residues within 4Å: Chain N: K.112, R.115, H.159, H.160, T.161, G.162, G.187 No protein-ligand interaction detected (PLIP)

13 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 7 residues within 4Å: Chain B: Y.64, Y.66, I.94, Y.116, I.193, R.196 Chain C: F.86 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.64, B:I.94, B:Y.116, B:I.193 Hydrogen bonds: B:R.196 MRD.7: 5 residues within 4Å: Chain D: Y.64, Y.66, Y.116, R.196 Chain E: F.86 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.64, D:Y.64, E:F.86 Hydrogen bonds: D:Y.66 MRD.8: 6 residues within 4Å: Chain D: R.115, H.159, H.160, T.161, G.162, G.187 No protein-ligand interaction detected (PLIP) MRD.9: 6 residues within 4Å: Chain D: T.161, G.162, Q.163, A.185, Y.186, G.187 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.162 MRD.11: 8 residues within 4Å: Chain E: Y.64, Y.66, S.92, I.94, Y.116, I.193, R.196 Chain F: F.86 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:Y.64, E:Y.64, E:I.94, E:Y.116, E:I.193, F:F.86 Hydrogen bonds: E:R.196 Water bridges: E:R.196 MRD.17: 6 residues within 4Å: Chain G: K.112, R.115, H.160, T.161, G.162, G.187 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.115, G:G.187 MRD.19: 5 residues within 4Å: Chain H: Y.64, S.92, I.94, Y.116, I.193 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:I.94, H:Y.116, H:I.193 Hydrogen bonds: H:S.92, H:S.92, H:Y.116 MRD.21: 5 residues within 4Å: Chain I: R.115, H.160, T.161, G.162, G.187 3 PLIP interactions: 3 interactions with chain I Water bridges: I:R.115, I:D.190, I:D.190 MRD.23: 6 residues within 4Å: Chain J: R.115, H.159, H.160, T.161, G.162, G.187 1 PLIP interactions: 1 interactions with chain J Water bridges: J:G.162 MRD.27: 6 residues within 4Å: Chain L: T.161, G.162, Q.163, A.185, Y.186, G.187 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.162 MRD.30: 7 residues within 4Å: Chain M: R.115, H.159, H.160, T.161, G.162, G.187 Ligands: MRD.31 No protein-ligand interaction detected (PLIP) MRD.31: 7 residues within 4Å: Chain M: T.161, G.162, Q.163, A.185, Y.186, G.187 Ligands: MRD.30 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:A.185 MRD.33: 5 residues within 4Å: Chain N: Y.64, Y.66, I.94, Y.116, I.193 4 PLIP interactions: 4 interactions with chain N Hydrophobic interactions: N:Y.64, N:Y.64, N:I.94, N:Y.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Open and compressed conformations of Francisella tularensis ClpP. Proteins (2017)

Release Date

2016-10-19

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
N

H
O

I
P

J
Q

K
R

L
S

M
T

N
U

ATP-dependent Clp protease proteolytic subunit

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