SMTL ID : 5g1s.2 (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

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

MRD.1: 4 residues within 4Å: Chain A: Y.64, Y.66, I.94, R.196 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.116 MRD.6: 7 residues within 4Å: Chain C: R.115, H.159, H.160, T.161, G.162, G.187 Ligands: MRD.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.159 Water bridges: C:R.115, C:G.162, C:D.190, C:D.190 MRD.7: 5 residues within 4Å: Chain C: T.161, G.162, Q.163, A.185 Ligands: MRD.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.162 MRD.10: 4 residues within 4Å: Chain D: R.115, H.160, T.161, G.187 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.115 Water bridges: D:H.160, D:I.189, D:D.190 MRD.16: 6 residues within 4Å: Chain A: F.86 Chain G: Y.64, Y.66, Y.116, I.193, R.196 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:Y.64, G:Y.64, G:I.193, A:F.86 Hydrogen bonds: G:R.196 MRD.19: 4 residues within 4Å: Chain H: Y.64, Y.66, I.94, R.196 2 PLIP interactions: 2 interactions with chain H Water bridges: H:Y.64, H:S.92 MRD.24: 7 residues within 4Å: Chain J: R.115, H.159, H.160, T.161, G.162, G.187 Ligands: MRD.25 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:H.159 Water bridges: J:R.115, J:G.162, J:D.190 MRD.25: 5 residues within 4Å: Chain J: T.161, G.162, Q.163, A.185 Ligands: MRD.24 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.162 MRD.28: 4 residues within 4Å: Chain K: R.115, H.160, T.161, G.187 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:R.115 Water bridges: K:H.160, K:I.189, K:D.190, K:D.190 MRD.34: 6 residues within 4Å: Chain H: F.86 Chain N: Y.64, Y.66, Y.116, I.193, R.196 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:Y.64, N:Y.64, N:I.193, H:F.86 Hydrogen bonds: N:R.196

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

ACT.2: 5 residues within 4Å: Chain A: S.101, S.104, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.104, 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:H.126, B:H.126, B:H.126 ACT.8: 6 residues within 4Å: Chain C: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.101, C:S.104, C:H.126, C:H.126 ACT.9: 6 residues within 4Å: Chain D: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.126, D:H.126 Salt bridges: D:H.126 ACT.12: 6 residues within 4Å: Chain E: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.104, E:L.105, E:H.126, E:H.126 ACT.15: 6 residues within 4Å: Chain F: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.104, F:H.126, F:H.126 Salt bridges: F:H.126 ACT.18: 6 residues within 4Å: Chain G: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:H.126, G:H.126 ACT.20: 5 residues within 4Å: Chain H: S.101, S.104, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.104, 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.26: 6 residues within 4Å: Chain J: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:S.101, J:S.104, J:H.126, J:H.126 ACT.27: 6 residues within 4Å: Chain K: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:H.126, K:H.126 Salt bridges: K:H.126 ACT.30: 6 residues within 4Å: Chain L: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:S.104, L:L.105, L:H.126, L:H.126 ACT.33: 6 residues within 4Å: Chain M: S.101, S.104, L.105, I.125, H.126, L.157 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:S.104, M:H.126, M:H.126 Salt bridges: M:H.126 ACT.36: 6 residues within 4Å: Chain N: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:H.126, N:H.126

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

MPD.3: 6 residues within 4Å: Chain B: K.112, R.115, H.160, T.161, G.162, G.187 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.112 MPD.5: 4 residues within 4Å: Chain C: Y.64, Y.66, Y.116, I.193 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.116, C:I.193 Water bridges: C:Y.66, C:S.92 MPD.11: 4 residues within 4Å: Chain E: R.115, H.160, T.161, G.162 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.115, E:H.160 MPD.13: 5 residues within 4Å: Chain F: Y.64, I.94, I.193, R.196 Chain G: F.86 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.64, F:I.94, F:I.193 Hydrogen bonds: F:R.196 MPD.14: 4 residues within 4Å: Chain F: T.161, G.162, Q.163, A.185 No protein-ligand interaction detected (PLIP) MPD.17: 6 residues within 4Å: Chain G: R.115, H.159, H.160, T.161, G.162, G.187 No protein-ligand interaction detected (PLIP) MPD.21: 6 residues within 4Å: Chain I: K.112, R.115, H.160, T.161, G.162, G.187 1 PLIP interactions: 1 interactions with chain I Water bridges: I:K.112 MPD.23: 4 residues within 4Å: Chain J: Y.64, Y.66, Y.116, I.193 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.116, J:I.193 Water bridges: J:Y.66, J:Y.66, J:S.92 MPD.29: 4 residues within 4Å: Chain L: R.115, H.160, T.161, G.162 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:R.115, L:H.160 Water bridges: L:D.190 MPD.31: 5 residues within 4Å: Chain M: Y.64, I.94, I.193, R.196 Chain N: F.86 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:Y.64, M:I.94, M:I.193 Hydrogen bonds: M:R.196 MPD.32: 4 residues within 4Å: Chain M: T.161, G.162, Q.163, A.185 No protein-ligand interaction detected (PLIP) MPD.35: 6 residues within 4Å: Chain N: R.115, H.159, H.160, T.161, G.162, G.187 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
D

E
E

F
F

G
G

H
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit

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