SMTL ID : 1tg6.1 (1 other biounit)

Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-heptamer

Ligands

6 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.1: 7 residues within 4Å: Chain A: Y.118, W.146, V.148, L.170 Chain G: L.104, T.135, Y.138 No protein-ligand interaction detected (PLIP) DIO.3: 6 residues within 4Å: Chain B: L.104, Y.138 Chain C: Y.118, W.146, V.148, L.170 No protein-ligand interaction detected (PLIP) DIO.11: 6 residues within 4Å: Chain C: L.104, Y.138 Chain D: Y.118, W.146, L.170, L.245 No protein-ligand interaction detected (PLIP) DIO.21: 6 residues within 4Å: Chain D: S.97, I.100 Chain E: C.86, M.88, Y.118, N.120 No protein-ligand interaction detected (PLIP) DIO.23: 7 residues within 4Å: Chain E: L.104, Y.138 Chain F: Y.118, W.146, V.148, L.170, L.245 No protein-ligand interaction detected (PLIP) DIO.26: 7 residues within 4Å: Chain F: L.104, Y.138 Chain G: Y.118, W.146, V.148, L.170 Ligands: EDO.27 No protein-ligand interaction detected (PLIP)

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: C.86, M.88, Y.118 Chain G: S.97, I.100 1 PLIP interactions: 1 interactions with chain G Water bridges: G:S.97 EDO.4: 6 residues within 4Å: Chain A: S.97, I.100 Chain B: C.86, M.88, N.120, V.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.87 Water bridges: B:N.120 EDO.5: 5 residues within 4Å: Chain A: Y.138 Chain B: Y.118, W.146, V.148, L.170 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain B: S.97 Chain C: C.86, M.88, Y.118, N.120 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:N.120 Hydrogen bonds: B:S.97 EDO.9: 4 residues within 4Å: Chain C: S.97, I.100 Chain D: C.86, Y.118 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain D: Y.138 Chain E: Y.118, W.146, V.148 No protein-ligand interaction detected (PLIP) EDO.24: 5 residues within 4Å: Chain E: S.97 Chain F: C.86, Y.118, N.120, V.148 1 PLIP interactions: 1 interactions with chain F Water bridges: F:N.120 EDO.27: 4 residues within 4Å: Chain G: H.116, Y.118, W.146 Ligands: DIO.26 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.118, G:Y.118

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: E.197, L.201 Chain B: R.174, Y.229, M.230, S.231 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:S.231, A:K.200, A:Q.204, A:Q.204, A:Q.204 GOL.7: 7 residues within 4Å: Chain B: E.197, K.200, L.201 Chain C: R.174, Y.229, M.230, S.231 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.200, B:K.200, B:Q.204 Water bridges: C:S.231, C:S.231 GOL.10: 8 residues within 4Å: Chain C: E.197, K.200, L.201, Q.204 Chain D: R.174, Y.229, M.230, S.231 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.204, D:Y.229 Water bridges: C:K.200, D:E.234 GOL.20: 7 residues within 4Å: Chain D: E.197, K.200, L.201 Chain E: R.174, Y.229, M.230, S.231 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.200, D:K.200 Water bridges: D:Q.204, E:S.231 GOL.22: 8 residues within 4Å: Chain E: E.197, K.200, L.201, Q.204 Chain F: R.174, Y.229, M.230, S.231 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain E Water bridges: F:S.231, F:S.231, E:Q.204 Hydrogen bonds: E:K.200, E:K.200, E:Q.204 GOL.25: 7 residues within 4Å: Chain F: E.197, K.200, Q.204 Chain G: R.174, Y.229, M.230, S.231 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:K.200, F:K.200, F:Q.204 Water bridges: G:S.231, G:S.231

7 x FME: N-FORMYLMETHIONINE(Non-covalent)

FME.13: 10 residues within 4Å: Chain A: P.122, G.123, G.124, V.126, S.153, M.154, H.178, Q.179, P.180, L.205 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.126 Hydrogen bonds: A:S.153 FME.14: 10 residues within 4Å: Chain B: G.123, G.124, V.126, S.153, M.154, H.178, Q.179, P.180, L.205, M.224 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.126 Hydrogen bonds: B:G.124, B:S.153, B:M.154 Water bridges: B:S.181 FME.15: 9 residues within 4Å: Chain C: G.123, G.124, V.126, S.153, M.154, H.178, Q.179, P.180, L.205 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.126 Hydrogen bonds: C:G.124, C:S.153, C:M.154 FME.16: 9 residues within 4Å: Chain D: G.123, G.124, V.126, S.153, M.154, H.178, Q.179, P.180, L.205 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.126 Hydrogen bonds: D:G.124, D:S.153, D:M.154 Water bridges: D:H.178, D:Q.179 FME.17: 10 residues within 4Å: Chain E: G.123, G.124, V.126, S.153, M.154, H.178, Q.179, P.180, L.205, M.224 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:V.126 Hydrogen bonds: E:G.124, E:S.153, E:M.154, E:H.178 FME.18: 8 residues within 4Å: Chain F: P.122, G.124, V.126, S.153, M.154, H.178, Q.179, P.180 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.126 Hydrogen bonds: F:G.124, F:S.153, F:H.178 FME.19: 10 residues within 4Å: Chain G: G.123, G.124, V.126, S.153, M.154, H.178, Q.179, P.180, L.205, M.224 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:V.126 Hydrogen bonds: G:G.124, G:S.153 Water bridges: G:H.178, G:H.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, S.G. et al., Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP. J.Struct.Biol. (2004)

Release Date

2005-03-22

Peptides

Putative ATP-dependent Clp protease proteolytic subunit: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Putative ATP-dependent Clp protease proteolytic subunit

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