SMTL ID : 6lt4.1

AAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

28 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.128 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.128 MG.4: 5 residues within 4Å: Chain A: T.454, G.457, K.458, T.459 Ligands: AGS.3 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: T.128 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.128 MG.8: 5 residues within 4Å: Chain B: T.454, G.457, K.458, T.459 Ligands: AGS.7 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: T.128 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.128 MG.12: 5 residues within 4Å: Chain C: T.454, G.457, K.458, T.459 Ligands: AGS.11 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: T.128 Ligands: AGS.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.128 MG.16: 5 residues within 4Å: Chain D: T.454, G.457, K.458, T.459 Ligands: AGS.15 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain E: T.128 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.128 MG.20: 5 residues within 4Å: Chain E: T.454, G.457, K.458, T.459 Ligands: AGS.19 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain F: T.128 Ligands: AGS.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.128 MG.24: 5 residues within 4Å: Chain F: T.454, G.457, K.458, T.459 Ligands: AGS.23 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain G: T.128 Ligands: AGS.26 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.128 MG.28: 5 residues within 4Å: Chain G: T.454, G.457, K.458, T.459 Ligands: AGS.27 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain H: T.128 Ligands: AGS.30 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.128 MG.32: 5 residues within 4Å: Chain H: T.454, G.457, K.458, T.459 Ligands: AGS.31 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain I: T.128 Ligands: AGS.34 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.128 MG.36: 5 residues within 4Å: Chain I: T.454, G.457, K.458, T.459 Ligands: AGS.35 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain J: T.128 Ligands: AGS.38 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.128 MG.40: 5 residues within 4Å: Chain J: T.454, G.457, K.458, T.459 Ligands: AGS.39 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain K: T.128 Ligands: AGS.42 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.128 MG.44: 5 residues within 4Å: Chain K: T.454, G.457, K.458, T.459 Ligands: AGS.43 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain L: T.128 Ligands: AGS.46 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.128 MG.48: 5 residues within 4Å: Chain L: T.454, G.457, K.458, T.459 Ligands: AGS.47 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain M: T.128 Ligands: AGS.50 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.128 MG.52: 5 residues within 4Å: Chain M: T.454, G.457, K.458, T.459 Ligands: AGS.51 No protein-ligand interaction detected (PLIP) MG.53: 2 residues within 4Å: Chain N: T.128 Ligands: AGS.54 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.128 MG.56: 5 residues within 4Å: Chain N: T.454, G.457, K.458, T.459 Ligands: AGS.55 No protein-ligand interaction detected (PLIP)

28 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 11 residues within 4Å: Chain A: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.96, A:I.96, A:G.124, A:V.125, A:G.126, A:G.126, A:K.127, A:T.128, A:A.129 AGS.3: 14 residues within 4Å: Chain A: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.418, A:Q.420, A:V.456, A:G.457, A:K.458, A:R.662 AGS.6: 11 residues within 4Å: Chain B: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.96, B:I.96, B:G.124, B:V.125, B:G.126, B:G.126, B:K.127, B:T.128, B:A.129 AGS.7: 14 residues within 4Å: Chain B: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.418, B:Q.420, B:V.456, B:G.457, B:K.458, B:R.662 AGS.10: 11 residues within 4Å: Chain C: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:I.96, C:I.96, C:G.124, C:V.125, C:G.126, C:G.126, C:K.127, C:T.128, C:A.129 AGS.11: 14 residues within 4Å: Chain C: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:I.418, C:Q.420, C:V.456, C:G.457, C:K.458, C:R.662 AGS.14: 11 residues within 4Å: Chain D: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:I.96, D:I.96, D:G.124, D:V.125, D:G.126, D:G.126, D:K.127, D:T.128, D:A.129 AGS.15: 14 residues within 4Å: Chain D: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.16 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:I.418, D:Q.420, D:T.454, D:V.456, D:G.457, D:K.458, D:R.662 AGS.18: 11 residues within 4Å: Chain E: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.17 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:I.96, E:I.96, E:G.124, E:V.125, E:G.126, E:G.126, E:K.127, E:T.128, E:A.129 AGS.19: 14 residues within 4Å: Chain E: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.20 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:I.418, E:Q.420, E:V.456, E:G.457, E:K.458, E:R.662 AGS.22: 11 residues within 4Å: Chain F: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.21 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:I.96, F:I.96, F:G.124, F:V.125, F:G.126, F:G.126, F:K.127, F:T.128, F:A.129 AGS.23: 14 residues within 4Å: Chain F: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.24 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:I.418, F:Q.420, F:V.456, F:G.457, F:K.458, F:R.662 AGS.26: 11 residues within 4Å: Chain G: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.25 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:I.96, G:I.96, G:G.124, G:V.125, G:G.126, G:G.126, G:K.127, G:T.128, G:A.129 AGS.27: 14 residues within 4Å: Chain G: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.28 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:I.418, G:Q.420, G:V.456, G:G.457, G:K.458, G:R.662 AGS.30: 11 residues within 4Å: Chain H: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.29 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:I.96, H:I.96, H:G.124, H:V.125, H:G.126, H:G.126, H:K.127, H:T.128, H:A.129 AGS.31: 14 residues within 4Å: Chain H: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.32 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:I.418, H:Q.420, H:V.456, H:G.457, H:K.458, H:E.460, H:R.662 AGS.34: 11 residues within 4Å: Chain I: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.33 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:I.96, I:I.96, I:G.124, I:V.125, I:G.126, I:G.126, I:K.127, I:T.128, I:A.129 AGS.35: 14 residues within 4Å: Chain I: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.36 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:I.418, I:Q.420, I:V.456, I:G.457, I:K.458, I:E.460, I:R.662 AGS.38: 11 residues within 4Å: Chain J: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.37 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:I.96, J:I.96, J:G.124, J:V.125, J:G.126, J:G.126, J:K.127, J:T.128, J:A.129 AGS.39: 14 residues within 4Å: Chain J: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.40 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:I.418, J:Q.420, J:V.456, J:G.457, J:K.458, J:E.460, J:R.662 AGS.42: 11 residues within 4Å: Chain K: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.41 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:I.96, K:I.96, K:G.124, K:V.125, K:G.126, K:G.126, K:K.127, K:T.128, K:A.129 AGS.43: 14 residues within 4Å: Chain K: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.44 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:I.418, K:Q.420, K:V.456, K:G.457, K:K.458, K:E.460, K:R.662 AGS.46: 11 residues within 4Å: Chain L: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.45 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:I.96, L:I.96, L:G.124, L:V.125, L:G.126, L:G.126, L:K.127, L:T.128, L:A.129 AGS.47: 14 residues within 4Å: Chain L: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.48 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:I.418, L:Q.420, L:V.456, L:G.457, L:K.458, L:E.460, L:R.662 AGS.50: 11 residues within 4Å: Chain M: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.49 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:I.96, M:I.96, M:G.124, M:V.125, M:G.126, M:G.126, M:K.127, M:T.128, M:A.129 AGS.51: 14 residues within 4Å: Chain M: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.52 7 PLIP interactions: 7 interactions with chain M Hydrogen bonds: M:I.418, M:Q.420, M:V.456, M:G.457, M:K.458, M:E.460, M:R.662 AGS.54: 11 residues within 4Å: Chain N: I.96, A.123, G.124, V.125, G.126, K.127, T.128, A.129, I.266, D.305 Ligands: MG.53 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:I.96, N:I.96, N:G.124, N:V.125, N:G.126, N:G.126, N:K.127, N:T.128, N:A.129 AGS.55: 14 residues within 4Å: Chain N: V.417, I.418, Q.420, T.454, G.455, V.456, G.457, K.458, T.459, E.460, I.618, V.658, R.662 Ligands: MG.56 7 PLIP interactions: 7 interactions with chain N Hydrogen bonds: N:I.418, N:Q.420, N:V.456, N:G.457, N:K.458, N:E.460, N:R.662

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, G. et al., ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones. Faseb J. (2020)

Release Date

2021-01-27

Peptides

ATP-dependent Clp protease, ATP-binding 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
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease, ATP-binding subunit

Related Entries With Identical Sequence