SMTL ID : 9cpk.1

D8 symmetry reconstruction of MmCPn in closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.91, G.92, K.161 Ligands: ADP.2, AF3.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.91 MG.5: 5 residues within 4Å: Chain B: D.91, G.92, K.161 Ligands: ADP.6, AF3.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.91 MG.9: 5 residues within 4Å: Chain C: D.91, G.92, K.161 Ligands: ADP.10, AF3.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.91 MG.13: 5 residues within 4Å: Chain D: D.91, G.92, K.161 Ligands: ADP.14, AF3.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.91 MG.17: 5 residues within 4Å: Chain E: D.91, G.92, K.161 Ligands: ADP.18, AF3.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.91 MG.21: 5 residues within 4Å: Chain F: D.91, G.92, K.161 Ligands: ADP.22, AF3.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.91 MG.25: 5 residues within 4Å: Chain G: D.91, G.92, K.161 Ligands: ADP.26, AF3.27 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.91 MG.29: 5 residues within 4Å: Chain H: D.91, G.92, K.161 Ligands: ADP.30, AF3.31 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.91 MG.33: 5 residues within 4Å: Chain I: D.91, G.92, K.161 Ligands: ADP.34, AF3.35 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.91 MG.37: 5 residues within 4Å: Chain J: D.91, G.92, K.161 Ligands: ADP.38, AF3.39 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.91 MG.41: 5 residues within 4Å: Chain K: D.91, G.92, K.161 Ligands: ADP.42, AF3.43 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.91 MG.45: 5 residues within 4Å: Chain L: D.91, G.92, K.161 Ligands: ADP.46, AF3.47 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.91 MG.49: 5 residues within 4Å: Chain M: D.91, G.92, K.161 Ligands: ADP.50, AF3.51 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.91 MG.53: 5 residues within 4Å: Chain N: D.91, G.92, K.161 Ligands: ADP.54, AF3.55 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.91 MG.57: 5 residues within 4Å: Chain O: D.91, G.92, K.161 Ligands: ADP.58, AF3.59 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.91 MG.61: 5 residues within 4Å: Chain P: D.91, G.92, K.161 Ligands: ADP.62, AF3.63 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.91

16 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 21 residues within 4Å: Chain A: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.1, AF3.3, K.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.40, A:G.92, A:G.92, A:T.93, A:T.94, A:T.95, A:T.95, A:G.404, A:G.405, A:E.490 Salt bridges: A:K.161 ADP.6: 21 residues within 4Å: Chain B: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.5, AF3.7, K.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.40, B:G.92, B:G.92, B:T.93, B:T.94, B:T.95, B:T.95, B:G.404, B:G.405, B:E.490 Salt bridges: B:K.161 ADP.10: 21 residues within 4Å: Chain C: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.9, AF3.11, K.12 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.40, C:G.92, C:G.92, C:T.93, C:T.94, C:T.95, C:T.95, C:G.404, C:G.405, C:E.490 Salt bridges: C:K.161 ADP.14: 21 residues within 4Å: Chain D: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.13, AF3.15, K.16 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.40, D:G.92, D:G.92, D:T.93, D:T.94, D:T.95, D:T.95, D:G.404, D:G.405, D:E.490 Salt bridges: D:K.161 ADP.18: 21 residues within 4Å: Chain E: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.17, AF3.19, K.20 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.40, E:G.92, E:G.92, E:T.93, E:T.94, E:T.95, E:T.95, E:G.404, E:G.405, E:E.490 Salt bridges: E:K.161 ADP.22: 21 residues within 4Å: Chain F: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.21, AF3.23, K.24 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.40, F:G.92, F:G.92, F:T.93, F:T.94, F:T.95, F:T.95, F:G.404, F:G.405, F:E.490 Salt bridges: F:K.161 ADP.26: 21 residues within 4Å: Chain G: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.25, AF3.27, K.28 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.40, G:G.92, G:G.92, G:T.93, G:T.94, G:T.95, G:T.95, G:G.404, G:G.405, G:E.490 Salt bridges: G:K.161 ADP.30: 21 residues within 4Å: Chain H: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.29, AF3.31, K.32 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.40, H:G.92, H:G.92, H:T.93, H:T.94, H:T.95, H:T.95, H:G.404, H:G.405, H:E.490 Salt bridges: H:K.161 ADP.34: 21 residues within 4Å: Chain I: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.33, AF3.35, K.36 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:G.40, I:G.92, I:G.92, I:T.93, I:T.94, I:T.94, I:T.95, I:G.404, I:G.405, I:E.490 Salt bridges: I:K.161 ADP.38: 21 residues within 4Å: Chain J: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.37, AF3.39, K.40 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.40, J:G.92, J:G.92, J:T.93, J:T.94, J:T.94, J:T.95, J:G.404, J:G.405, J:E.490 Salt bridges: J:K.161 ADP.42: 21 residues within 4Å: Chain K: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.41, AF3.43, K.44 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:G.40, K:G.92, K:G.92, K:T.93, K:T.94, K:T.94, K:T.95, K:G.404, K:G.405, K:E.490 Salt bridges: K:K.161 ADP.46: 21 residues within 4Å: Chain L: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.45, AF3.47, K.48 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:G.40, L:G.92, L:G.92, L:T.93, L:T.94, L:T.94, L:T.95, L:G.404, L:G.405, L:E.490 Salt bridges: L:K.161 ADP.50: 21 residues within 4Å: Chain M: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.49, AF3.51, K.52 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:G.40, M:G.92, M:G.92, M:T.93, M:T.94, M:T.94, M:T.95, M:G.404, M:G.405, M:E.490 Salt bridges: M:K.161 ADP.54: 21 residues within 4Å: Chain N: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.53, AF3.55, K.56 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:G.40, N:G.92, N:G.92, N:T.93, N:T.94, N:T.94, N:T.95, N:G.404, N:G.405, N:E.490 Salt bridges: N:K.161 ADP.58: 21 residues within 4Å: Chain O: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.57, AF3.59, K.60 11 PLIP interactions: 11 interactions with chain O Hydrogen bonds: O:G.40, O:G.92, O:G.92, O:T.93, O:T.94, O:T.94, O:T.95, O:G.404, O:G.405, O:E.490 Salt bridges: O:K.161 ADP.62: 21 residues within 4Å: Chain P: T.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, T.95, G.403, G.404, G.405, L.473, V.475, F.476, M.483, V.488, E.490 Ligands: MG.61, AF3.63, K.64 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:G.40, P:G.92, P:G.92, P:T.93, P:T.94, P:T.94, P:T.95, P:G.404, P:G.405, P:E.490 Salt bridges: P:K.161

16 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 9 residues within 4Å: Chain A: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.1, ADP.2 No protein-ligand interaction detected (PLIP) AF3.7: 9 residues within 4Å: Chain B: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.5, ADP.6 No protein-ligand interaction detected (PLIP) AF3.11: 9 residues within 4Å: Chain C: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.9, ADP.10 No protein-ligand interaction detected (PLIP) AF3.15: 9 residues within 4Å: Chain D: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.13, ADP.14 No protein-ligand interaction detected (PLIP) AF3.19: 9 residues within 4Å: Chain E: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.17, ADP.18 No protein-ligand interaction detected (PLIP) AF3.23: 9 residues within 4Å: Chain F: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.21, ADP.22 No protein-ligand interaction detected (PLIP) AF3.27: 9 residues within 4Å: Chain G: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.25, ADP.26 No protein-ligand interaction detected (PLIP) AF3.31: 9 residues within 4Å: Chain H: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.29, ADP.30 No protein-ligand interaction detected (PLIP) AF3.35: 9 residues within 4Å: Chain I: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.33, ADP.34 No protein-ligand interaction detected (PLIP) AF3.39: 9 residues within 4Å: Chain J: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.37, ADP.38 No protein-ligand interaction detected (PLIP) AF3.43: 9 residues within 4Å: Chain K: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.41, ADP.42 No protein-ligand interaction detected (PLIP) AF3.47: 9 residues within 4Å: Chain L: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.45, ADP.46 No protein-ligand interaction detected (PLIP) AF3.51: 9 residues within 4Å: Chain M: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.49, ADP.50 No protein-ligand interaction detected (PLIP) AF3.55: 9 residues within 4Å: Chain N: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.53, ADP.54 No protein-ligand interaction detected (PLIP) AF3.59: 9 residues within 4Å: Chain O: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.57, ADP.58 No protein-ligand interaction detected (PLIP) AF3.63: 9 residues within 4Å: Chain P: D.60, G.61, D.91, G.92, T.93, T.94, K.161 Ligands: MG.61, ADP.62 No protein-ligand interaction detected (PLIP)

16 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: T.38, G.40, N.59, G.160 Ligands: ADP.2 Ligand excluded by PLIP K.8: 5 residues within 4Å: Chain B: T.38, G.40, N.59, G.160 Ligands: ADP.6 Ligand excluded by PLIP K.12: 5 residues within 4Å: Chain C: T.38, G.40, N.59, G.160 Ligands: ADP.10 Ligand excluded by PLIP K.16: 5 residues within 4Å: Chain D: T.38, G.40, N.59, G.160 Ligands: ADP.14 Ligand excluded by PLIP K.20: 5 residues within 4Å: Chain E: T.38, G.40, N.59, G.160 Ligands: ADP.18 Ligand excluded by PLIP K.24: 5 residues within 4Å: Chain F: T.38, G.40, N.59, G.160 Ligands: ADP.22 Ligand excluded by PLIP K.28: 5 residues within 4Å: Chain G: T.38, G.40, N.59, G.160 Ligands: ADP.26 Ligand excluded by PLIP K.32: 5 residues within 4Å: Chain H: T.38, G.40, N.59, G.160 Ligands: ADP.30 Ligand excluded by PLIP K.36: 5 residues within 4Å: Chain I: T.38, G.40, N.59, G.160 Ligands: ADP.34 Ligand excluded by PLIP K.40: 5 residues within 4Å: Chain J: T.38, G.40, N.59, G.160 Ligands: ADP.38 Ligand excluded by PLIP K.44: 5 residues within 4Å: Chain K: T.38, G.40, N.59, G.160 Ligands: ADP.42 Ligand excluded by PLIP K.48: 5 residues within 4Å: Chain L: T.38, G.40, N.59, G.160 Ligands: ADP.46 Ligand excluded by PLIP K.52: 5 residues within 4Å: Chain M: T.38, G.40, N.59, G.160 Ligands: ADP.50 Ligand excluded by PLIP K.56: 5 residues within 4Å: Chain N: T.38, G.40, N.59, G.160 Ligands: ADP.54 Ligand excluded by PLIP K.60: 5 residues within 4Å: Chain O: T.38, G.40, N.59, G.160 Ligands: ADP.58 Ligand excluded by PLIP K.64: 5 residues within 4Å: Chain P: T.38, G.40, N.59, G.160 Ligands: ADP.62 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanyan, Z., Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution. To Be Published

Release Date

2025-07-30

Peptides

Chaperonin: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
J

C
K

D
L

E
M

F
A

G
C

H
D

I
N

J
E

K
F

L
G

M
H

N
I

O
O

P
P

Chaperonin

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