SMTL ID : 8wux.1

Cryo-EM structure of H. thermophilus GroEL-GroES bullet complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.86 Ligands: ANP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.86, A:D.86 MG.3: 3 residues within 4Å: Chain B: D.86, S.150 Ligands: ANP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.86, B:D.86 MG.6: 2 residues within 4Å: Chain D: D.86 Ligands: ANP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.86, D:D.86 MG.8: 2 residues within 4Å: Chain E: D.86 Ligands: ANP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.86, E:D.86 MG.11: 2 residues within 4Å: Chain G: D.86 Ligands: ANP.12 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.86, G:D.86 MG.13: 2 residues within 4Å: Chain H: D.86 Ligands: ANP.15 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.86, H:D.86 MG.16: 2 residues within 4Å: Chain J: D.86 Ligands: ANP.17 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.86, J:D.86 MG.18: 2 residues within 4Å: Chain K: D.86 Ligands: ANP.20 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.86, K:D.86 MG.21: 2 residues within 4Å: Chain M: D.86 Ligands: ANP.22 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.86, M:D.86 MG.23: 2 residues within 4Å: Chain N: D.86 Ligands: ANP.25 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.86, N:D.86 MG.26: 2 residues within 4Å: Chain P: D.86 Ligands: ANP.27 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.86 MG.28: 2 residues within 4Å: Chain Q: D.86 Ligands: ANP.30 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.86 MG.31: 2 residues within 4Å: Chain S: D.86 Ligands: ANP.32 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:D.86 MG.33: 2 residues within 4Å: Chain T: D.86 Ligands: ANP.35 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:D.86, T:D.86

14 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 25 residues within 4Å: Chain A: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.31, A:D.51, A:D.51, A:G.52, A:G.87, A:G.87, A:T.88, A:T.89, A:T.89, A:T.89, A:T.90, A:N.153, A:G.414, A:G.415, A:D.482, A:D.482, A:A.483, A:G.484, A:D.498, A:D.498 Salt bridges: A:K.50 ANP.5: 24 residues within 4Å: Chain B: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.3, K.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.31, B:D.51, B:V.53, B:G.87, B:G.87, B:T.88, B:T.88, B:T.89, B:T.90, B:N.153, B:G.414, B:D.482, B:D.482, B:A.483, B:G.484, B:D.498 ANP.7: 25 residues within 4Å: Chain D: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:G.31, D:D.51, D:G.52, D:G.87, D:G.87, D:T.88, D:T.89, D:T.89, D:T.89, D:T.90, D:N.153, D:G.414, D:G.415, D:D.482, D:D.482, D:A.483, D:G.484, D:D.498, D:D.498 Salt bridges: D:K.50 ANP.10: 24 residues within 4Å: Chain E: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.8, K.9 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.31, E:D.51, E:V.53, E:G.87, E:G.87, E:T.88, E:T.88, E:T.89, E:T.89, E:T.90, E:N.153, E:G.414, E:D.482, E:D.482, E:A.483, E:G.484, E:D.498 ANP.12: 26 residues within 4Å: Chain G: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, D.397, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.11 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:G.31, G:G.52, G:G.87, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:N.153, G:D.397, G:G.414, G:G.415, G:D.482, G:A.483, G:G.484, G:D.498, G:D.498 Salt bridges: G:K.50 ANP.15: 24 residues within 4Å: Chain H: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.13, K.14 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:G.31, H:D.51, H:V.53, H:G.87, H:G.87, H:T.88, H:T.88, H:T.89, H:T.90, H:N.153, H:G.414, H:D.482, H:D.482, H:A.483, H:G.484, H:D.498 ANP.17: 25 residues within 4Å: Chain J: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.16 19 PLIP interactions: 19 interactions with chain J Hydrogen bonds: J:G.31, J:D.51, J:D.51, J:G.52, J:G.87, J:G.87, J:T.88, J:T.89, J:T.89, J:T.89, J:T.90, J:N.153, J:G.414, J:G.415, J:D.482, J:A.483, J:G.484, J:D.498 Salt bridges: J:K.50 ANP.20: 24 residues within 4Å: Chain K: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.18, K.19 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:G.31, K:D.51, K:V.53, K:G.87, K:G.87, K:T.88, K:T.88, K:T.89, K:T.90, K:N.153, K:G.414, K:D.482, K:D.482, K:A.483, K:G.484, K:D.498 ANP.22: 25 residues within 4Å: Chain M: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.21 20 PLIP interactions: 20 interactions with chain M Hydrogen bonds: M:G.31, M:D.51, M:G.52, M:G.87, M:G.87, M:T.88, M:T.89, M:T.89, M:T.89, M:T.90, M:N.153, M:G.414, M:G.415, M:D.482, M:D.482, M:A.483, M:G.484, M:D.498, M:D.498 Salt bridges: M:K.50 ANP.25: 24 residues within 4Å: Chain N: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.23, K.24 16 PLIP interactions: 16 interactions with chain N Hydrogen bonds: N:G.31, N:D.51, N:V.53, N:G.87, N:G.87, N:T.88, N:T.88, N:T.89, N:T.90, N:N.153, N:G.414, N:D.482, N:D.482, N:A.483, N:G.484, N:D.498 ANP.27: 25 residues within 4Å: Chain P: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.26 17 PLIP interactions: 17 interactions with chain P Hydrogen bonds: P:G.31, P:G.52, P:G.87, P:G.87, P:T.88, P:T.89, P:T.89, P:T.89, P:T.90, P:N.153, P:G.414, P:G.415, P:D.482, P:A.483, P:G.484, P:D.498 Salt bridges: P:K.50 ANP.30: 24 residues within 4Å: Chain Q: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.28, K.29 17 PLIP interactions: 17 interactions with chain Q Hydrogen bonds: Q:G.31, Q:D.51, Q:V.53, Q:G.87, Q:G.87, Q:T.88, Q:T.88, Q:T.89, Q:T.90, Q:N.153, Q:G.414, Q:G.415, Q:D.482, Q:D.482, Q:A.483, Q:G.484, Q:D.498 ANP.32: 25 residues within 4Å: Chain S: T.29, L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, G.415, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.31 18 PLIP interactions: 18 interactions with chain S Hydrogen bonds: S:G.31, S:G.52, S:G.87, S:G.87, S:T.88, S:T.89, S:T.89, S:T.89, S:T.90, S:N.153, S:G.414, S:G.415, S:D.482, S:D.482, S:A.483, S:G.484, S:D.498 Salt bridges: S:K.50 ANP.35: 24 residues within 4Å: Chain T: T.29, L.30, G.31, P.32, D.51, V.53, D.86, G.87, T.88, T.89, T.90, I.149, N.153, G.413, G.414, I.453, F.481, D.482, A.483, G.484, I.496, D.498 Ligands: MG.33, K.34 18 PLIP interactions: 18 interactions with chain T Hydrogen bonds: T:G.31, T:D.51, T:V.53, T:D.86, T:G.87, T:G.87, T:T.88, T:T.88, T:T.89, T:T.90, T:N.153, T:G.414, T:G.415, T:D.482, T:D.482, T:A.483, T:G.484, T:D.498

7 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain B: T.29, G.31, K.50 Ligands: ANP.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.29, B:G.31, B:K.50 K.9: 4 residues within 4Å: Chain E: T.29, G.31, K.50 Ligands: ANP.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.29, E:G.31, E:K.50 K.14: 4 residues within 4Å: Chain H: T.29, G.31, K.50 Ligands: ANP.15 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:T.29, H:G.31, H:K.50 K.19: 4 residues within 4Å: Chain K: T.29, G.31, K.50 Ligands: ANP.20 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:T.29, K:G.31, K:K.50 K.24: 4 residues within 4Å: Chain N: T.29, G.31, K.50 Ligands: ANP.25 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:T.29, N:G.31, N:K.50 K.29: 4 residues within 4Å: Chain Q: T.29, G.31, K.50 Ligands: ANP.30 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:T.29, Q:G.31, Q:K.50 K.34: 4 residues within 4Å: Chain T: T.29, G.31, K.50 Ligands: ANP.35 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:T.29, T:G.31, T:K.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, Z. et al., Structural insights into thermophilic chaperonin complexes. Structure (2024)

Release Date

2024-03-27

Peptides

Chaperonin GroEL: ABDEGHJKMNPQST
Co-chaperonin GroES: CFILORU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

D
B

E
I

G
C

H
J

J
D

K
K

M
E

N
L

P
F

Q
M

S
G

T
N

C
a

F
b

I
c

L
d

O
e

R
f

U
g

Chaperonin GroEL

Co-chaperonin GroES

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