SMTL ID : 8baa.1

CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-1-mer

Ligands

7 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.1: 8 residues within 4Å: Chain A: G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.2, ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 AF3.5: 9 residues within 4Å: Chain B: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.4, ADP.6 No protein-ligand interaction detected (PLIP) AF3.8: 9 residues within 4Å: Chain C: D.51, G.85, D.86, G.87, T.88, T.89, D.397 Ligands: MG.7, ADP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 AF3.11: 9 residues within 4Å: Chain D: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.10, MG.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.86, D:D.397 AF3.13: 9 residues within 4Å: Chain E: D.51, G.85, D.86, G.87, T.88, T.89, D.397 Ligands: MG.14, ADP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.86 AF3.16: 9 residues within 4Å: Chain F: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.17, ADP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 AF3.19: 8 residues within 4Å: Chain G: D.51, D.86, G.87, T.88, T.89, D.397 Ligands: ADP.20, MG.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.86, G:D.397

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.86, G.87 Ligands: AF3.1, ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 MG.4: 4 residues within 4Å: Chain B: D.86, G.87 Ligands: AF3.5, ADP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.86, B:D.86 MG.7: 4 residues within 4Å: Chain C: D.86, G.87 Ligands: AF3.8, ADP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.86, C:D.86 MG.12: 4 residues within 4Å: Chain D: D.86, G.87 Ligands: ADP.10, AF3.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.14: 4 residues within 4Å: Chain E: D.86, G.87 Ligands: AF3.13, ADP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.86 MG.17: 5 residues within 4Å: Chain F: D.86, G.87, S.150 Ligands: AF3.16, ADP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.86, F:D.86 MG.21: 5 residues within 4Å: Chain G: D.86, G.87, D.397 Ligands: AF3.19, ADP.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86 MG.22: 3 residues within 4Å: Chain H: D.86, G.87 Ligands: ADP.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.86, H:D.86 MG.25: 2 residues within 4Å: Chain I: D.86 Ligands: ADP.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.86, I:D.86 MG.30: 3 residues within 4Å: Chain J: D.86, G.87 Ligands: ADP.28 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.86, J:D.86 MG.33: 3 residues within 4Å: Chain K: D.86, G.87 Ligands: ADP.32 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.86, K:D.86 MG.35: 3 residues within 4Å: Chain L: D.86, G.87 Ligands: ADP.36 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.86, L:D.86 MG.37: 2 residues within 4Å: Chain M: D.86 Ligands: ADP.39 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.86, M:D.86 MG.42: 3 residues within 4Å: Chain N: D.86, G.87 Ligands: ADP.40 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.86, N:D.86

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

ADP.3: 23 residues within 4Å: Chain A: L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.153, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: AF3.1, MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.87, A:T.88, A:T.88, A:T.89, A:T.89, A:T.90, A:G.414, A:N.478, A:A.479, A:A.480, A:D.494, A:D.494 Salt bridges: A:K.50 ADP.6: 24 residues within 4Å: Chain B: L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.150, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: MG.4, AF3.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.31, B:G.87, B:T.88, B:T.88, B:T.89, B:G.414, B:N.478, B:A.479, B:A.480, B:D.494 Salt bridges: B:K.50 ADP.9: 23 residues within 4Å: Chain C: L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: MG.7, AF3.8 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.31, C:G.87, C:G.87, C:T.89, C:T.90, C:T.90, C:G.414, C:N.478, C:A.479, C:A.480, C:D.494, C:D.494 Salt bridges: C:K.50 ADP.10: 23 residues within 4Å: Chain D: L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, S.153, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: AF3.11, MG.12 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.31, D:G.87, D:G.87, D:T.88, D:T.89, D:T.89, D:T.90, D:T.90, D:G.414, D:G.415, D:N.478, D:A.479, D:A.480, D:D.494, D:D.494 Salt bridges: D:K.50 ADP.15: 23 residues within 4Å: Chain E: L.30, G.31, P.32, K.50, D.51, G.52, D.86, G.87, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: AF3.13, MG.14 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.87, E:T.89, E:T.89, E:T.90, E:G.414, E:N.478, E:A.479, E:A.480, E:D.494, E:D.494 Salt bridges: E:K.50 ADP.18: 23 residues within 4Å: Chain F: L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: AF3.16, MG.17 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.31, F:G.87, F:G.87, F:T.88, F:T.89, F:T.89, F:T.90, F:T.90, F:G.414, F:N.478, F:A.479, F:A.480, F:D.494, F:D.494 Salt bridges: F:K.50 ADP.20: 25 residues within 4Å: Chain G: L.30, G.31, P.32, K.50, D.86, G.87, T.88, T.89, T.90, I.149, N.152, S.153, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, M.487, I.492, D.494 Ligands: AF3.19, MG.21 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:D.86, G:G.87, G:G.87, G:T.88, G:T.89, G:T.89, G:T.90, G:T.90, G:G.414, G:N.478, G:A.479, G:A.480, G:D.494, G:D.494 Salt bridges: G:K.50 ADP.23: 20 residues within 4Å: Chain H: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, S.153, G.413, G.414, I.453, N.478, A.479, A.480, I.492, D.494 Ligands: MG.22, K.24 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.31, H:D.86, H:G.87, H:T.89, H:T.89, H:T.90, H:T.90, H:G.414, H:N.478, H:A.479, H:A.480 ADP.26: 21 residues within 4Å: Chain I: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.25, K.27 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:G.31, I:D.86, I:D.86, I:G.87, I:T.89, I:T.89, I:G.414, I:N.478, I:A.479, I:A.480, I:D.494 ADP.28: 21 residues within 4Å: Chain J: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.29, MG.30 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:G.31, J:D.86, J:G.87, J:T.88, J:T.89, J:T.89, J:T.90, J:G.414, J:N.478, J:A.479, J:A.480, J:D.494, J:D.494 ADP.32: 21 residues within 4Å: Chain K: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.31, MG.33 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:G.31, K:D.86, K:G.87, K:T.88, K:T.89, K:T.89, K:T.90, K:G.414, K:N.478, K:A.479, K:A.480, K:D.494, K:D.494 ADP.36: 21 residues within 4Å: Chain L: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.34, MG.35 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:G.31, L:D.86, L:G.87, L:T.88, L:T.89, L:T.89, L:T.90, L:G.414, L:N.478, L:A.479, L:A.480, L:D.494, L:D.494 ADP.39: 20 residues within 4Å: Chain M: L.30, G.31, P.32, D.86, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: MG.37, K.38 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:G.31, M:D.86, M:T.89, M:T.89, M:T.90, M:G.414, M:N.478, M:A.479, M:A.480, M:D.494 ADP.40: 21 residues within 4Å: Chain N: L.30, G.31, P.32, D.86, G.87, T.88, T.89, T.90, I.149, G.413, G.414, G.415, I.453, Y.477, N.478, A.479, A.480, I.492, D.494 Ligands: K.41, MG.42 13 PLIP interactions: 13 interactions with chain N Hydrogen bonds: N:G.31, N:D.86, N:G.87, N:T.89, N:T.89, N:T.90, N:T.90, N:G.414, N:N.478, N:A.479, N:A.480, N:D.494, N:D.494

7 x K: POTASSIUM ION(Non-covalent)

K.24: 3 residues within 4Å: Chain H: G.31, P.32 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:G.31 K.27: 3 residues within 4Å: Chain I: G.31, N.152 Ligands: ADP.26 No protein-ligand interaction detected (PLIP) K.29: 4 residues within 4Å: Chain J: T.29, G.31, K.50 Ligands: ADP.28 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.29, J:G.31 K.31: 4 residues within 4Å: Chain K: T.29, G.31, K.50 Ligands: ADP.32 No protein-ligand interaction detected (PLIP) K.34: 4 residues within 4Å: Chain L: T.29, L.30, G.31 Ligands: ADP.36 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.29, L:G.31 K.38: 4 residues within 4Å: Chain M: T.29, G.31, G.34 Ligands: ADP.39 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.29, M:G.31 K.41: 4 residues within 4Å: Chain N: T.29, G.31, P.32 Ligands: ADP.40 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:G.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gardner, S. et al., CryoEM snapshots of non-native Rubisco bound to GroEL, GroEL-ADP.BeF3, and GroEL-GroES. To Be Published

Release Date

2025-02-12

Peptides

Chaperonin GroEL: ABCDEFGHIJKLMN
Co-chaperonin GroES: OPQRSTU
Ribulose bisphosphate carboxylase: V

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

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
Z

Chaperonin GroEL

Co-chaperonin GroES

Ribulose bisphosphate carboxylase

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