SMTL ID : 1tg6.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-14-mer

Ligands

12 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) DIO.28: 7 residues within 4Å: Chain H: Y.118, W.146, V.148, L.170 Chain N: L.104, T.135, Y.138 No protein-ligand interaction detected (PLIP) DIO.30: 6 residues within 4Å: Chain I: L.104, Y.138 Chain J: Y.118, W.146, V.148, L.170 No protein-ligand interaction detected (PLIP) DIO.38: 6 residues within 4Å: Chain J: L.104, Y.138 Chain K: Y.118, W.146, L.170, L.245 No protein-ligand interaction detected (PLIP) DIO.48: 6 residues within 4Å: Chain K: S.97, I.100 Chain L: C.86, M.88, Y.118, N.120 No protein-ligand interaction detected (PLIP) DIO.50: 7 residues within 4Å: Chain L: L.104, Y.138 Chain M: Y.118, W.146, V.148, L.170, L.245 1 PLIP interactions: 1 interactions with chain M Water bridges: M:Y.118 DIO.53: 7 residues within 4Å: Chain M: L.104, Y.138 Chain N: Y.118, W.146, V.148, L.170 Ligands: EDO.54 No protein-ligand interaction detected (PLIP)

16 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 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: S.97, I.100 Chain B: C.86, M.88, N.120, V.148 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Y.138 Chain B: Y.118, W.146, V.148, L.170 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: S.97 Chain C: C.86, M.88, Y.118, N.120 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain C: S.97, I.100 Chain D: C.86, Y.118 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain D: Y.138 Chain E: Y.118, W.146, V.148 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain E: S.97 Chain F: C.86, Y.118, N.120, V.148 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain G: H.116, Y.118, W.146 Ligands: DIO.26 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain H: C.86, M.88, Y.118 Chain N: S.97, I.100 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain H: S.97, I.100 Chain I: C.86, M.88, N.120, V.148 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain H: Y.138 Chain I: Y.118, W.146, V.148, L.170 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain I: S.97 Chain J: C.86, M.88, Y.118, N.120 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain J: S.97, I.100 Chain K: C.86, Y.118 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain K: Y.138 Chain L: Y.118, W.146, V.148 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain L: S.97 Chain M: C.86, Y.118, N.120, V.148 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain N: H.116, Y.118, W.146 Ligands: DIO.53 Ligand excluded by PLIP

12 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 D, 2 interactions with chain C Hydrogen bonds: D:Y.229, C:Q.204 Water bridges: D:E.234, C:K.200 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: 4 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:K.200, E:K.200, E:Q.204 Water bridges: E:Q.204, F:S.231, F:S.231 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 GOL.33: 6 residues within 4Å: Chain H: E.197, L.201 Chain I: R.174, Y.229, M.230, S.231 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain I Water bridges: H:E.197, H:K.200, H:Q.204, H:Q.204, H:Q.204, I:S.231 GOL.34: 7 residues within 4Å: Chain I: E.197, K.200, L.201 Chain J: R.174, Y.229, M.230, S.231 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:K.200, I:K.200, I:Q.204 Water bridges: I:E.197, J:S.231, J:S.231 GOL.37: 8 residues within 4Å: Chain J: E.197, K.200, L.201, Q.204 Chain K: R.174, Y.229, M.230, S.231 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:Q.204, K:Y.229 Water bridges: J:E.197, J:K.200, K:E.234 GOL.47: 7 residues within 4Å: Chain K: E.197, K.200, L.201 Chain L: R.174, Y.229, M.230, S.231 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:K.200, K:K.200 Water bridges: K:E.197, K:Q.204, L:S.231 GOL.49: 8 residues within 4Å: Chain L: E.197, K.200, L.201, Q.204 Chain M: R.174, Y.229, M.230, S.231 7 PLIP interactions: 5 interactions with chain L, 2 interactions with chain M Hydrogen bonds: L:K.200, L:K.200, L:Q.204 Water bridges: L:E.197, L:Q.204, M:S.231, M:S.231 GOL.52: 7 residues within 4Å: Chain M: E.197, K.200, Q.204 Chain N: R.174, Y.229, M.230, S.231 6 PLIP interactions: 2 interactions with chain N, 4 interactions with chain M Water bridges: N:S.231, N:S.231, M:E.197 Hydrogen bonds: M:K.200, M:K.200, M:Q.204

14 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 FME.40: 10 residues within 4Å: Chain H: 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 H Hydrophobic interactions: H:V.126 Hydrogen bonds: H:S.153 FME.41: 10 residues within 4Å: Chain I: 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 I Hydrophobic interactions: I:V.126 Hydrogen bonds: I:G.124, I:S.153, I:M.154 Water bridges: I:S.181 FME.42: 9 residues within 4Å: Chain J: 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 J Hydrophobic interactions: J:V.126 Hydrogen bonds: J:G.124, J:S.153, J:M.154 FME.43: 9 residues within 4Å: Chain K: 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 K Hydrophobic interactions: K:V.126 Hydrogen bonds: K:G.124, K:S.153, K:M.154 Water bridges: K:H.178, K:Q.179 FME.44: 10 residues within 4Å: Chain L: 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 L Hydrophobic interactions: L:V.126 Hydrogen bonds: L:G.124, L:S.153, L:M.154, L:H.178 FME.45: 8 residues within 4Å: Chain M: P.122, G.124, V.126, S.153, M.154, H.178, Q.179, P.180 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:V.126 Hydrogen bonds: M:G.124, M:S.153, M:H.178 FME.46: 10 residues within 4Å: Chain N: 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 N Hydrophobic interactions: N:V.126 Hydrogen bonds: N:G.124, N:S.153 Water bridges: N:H.178, N:Q.179

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: 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

Putative ATP-dependent Clp protease proteolytic subunit

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