SMTL ID : 5g1r.1

Open conformation of Francisella tularensis ClpP at 1.9 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

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

MPD.1: 6 residues within 4Å: Chain A: Y.64, Y.66, I.94, Y.116, R.196 Chain B: F.86 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.64, A:I.94, A:Y.116, B:F.86 Water bridges: A:Y.116 MPD.9: 8 residues within 4Å: Chain E: Y.64, Y.66, S.92, I.94, Y.116, I.193, R.196 Chain F: F.86 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.64, E:I.94, E:Y.116, E:Y.116, E:I.193 Hydrogen bonds: E:R.196 MPD.10: 6 residues within 4Å: Chain F: Y.64, Y.66, I.94, Y.116, I.193, R.196 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.94, F:Y.116, F:Y.116 Hydrogen bonds: F:Y.66 Water bridges: F:R.196, F:R.196 MPD.13: 6 residues within 4Å: Chain H: Y.64, Y.66, I.94, Y.116, R.196 Chain I: F.86 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:Y.64, H:I.94, H:Y.116, I:F.86 Water bridges: H:Y.116 MPD.21: 8 residues within 4Å: Chain L: Y.64, Y.66, S.92, I.94, Y.116, I.193, R.196 Chain M: F.86 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:Y.64, L:I.94, L:Y.116, L:Y.116, L:I.193 Hydrogen bonds: L:R.196 MPD.22: 6 residues within 4Å: Chain M: Y.64, Y.66, I.94, Y.116, I.193, R.196 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:I.94, M:Y.116, M:Y.116 Hydrogen bonds: M:Y.66 Water bridges: M:R.196, M:R.196

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

ACT.2: 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: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:S.104, B:L.105, B:H.126 ACT.5: 4 residues within 4Å: Chain B: Y.24, F.34, N.36 Chain C: N.45 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.24 Water bridges: B:N.36 ACT.7: 7 residues within 4Å: Chain C: S.101, M.102, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.104, C:H.126 ACT.8: 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:S.101, D:L.105, D:H.126 ACT.11: 6 residues within 4Å: Chain F: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.104, F:H.126 ACT.12: 6 residues within 4Å: Chain G: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.101, G:L.105, G:H.126 ACT.14: 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:S.104, H:H.126 ACT.16: 6 residues within 4Å: Chain I: S.101, S.104, L.105, I.125, H.126, L.157 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:S.104, I:L.105, I:H.126 ACT.17: 4 residues within 4Å: Chain I: Y.24, F.34, N.36 Chain J: N.45 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.24 Water bridges: I:N.36 ACT.19: 7 residues within 4Å: Chain J: S.101, M.102, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:S.104, J:H.126 ACT.20: 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:S.101, K:L.105, K:H.126 ACT.23: 6 residues within 4Å: Chain M: S.101, S.104, L.105, I.125, H.126, L.157 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:S.104, M:H.126 ACT.24: 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.101, N:L.105, N:H.126

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

MRD.3: 6 residues within 4Å: Chain B: Y.64, Y.66, Y.116, I.193, R.196 Chain C: F.86 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.64, B:I.193 Water bridges: B:Y.116 MRD.6: 3 residues within 4Å: Chain C: Y.64, Y.66, I.193 No protein-ligand interaction detected (PLIP) MRD.15: 6 residues within 4Å: Chain I: Y.64, Y.66, Y.116, I.193, R.196 Chain J: F.86 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:Y.64, I:I.193 Water bridges: I:Y.116 MRD.18: 3 residues within 4Å: Chain J: Y.64, Y.66, I.193 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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