SMTL ID : 4pkn.1

Crystal structure of the football-shaped GroEL-GroES2-(ADPBeFx)14 complex containing substrate Rubisco

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.66 Å

Oligo State

hetero-14-14-mer

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.2, MG.3, K.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.30, A:G.32, A:G.88, A:G.88, A:T.89, A:T.90, A:T.91, A:T.91, A:G.415, A:N.479, A:A.480, A:A.481, A:D.495 Salt bridges: A:K.51 ADP.5: 22 residues within 4Å: Chain B: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.6, MG.7, K.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.30, B:G.32, B:G.88, B:G.88, B:T.90, B:T.90, B:T.91, B:T.91, B:T.91, B:G.415, B:N.479, B:A.480, B:A.481, B:D.495 Salt bridges: B:K.51 ADP.9: 21 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, D.495 Ligands: BEF.10, MG.11, K.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.30, C:G.32, C:G.88, C:G.88, C:T.90, C:T.90, C:T.91, C:T.91, C:G.415, C:N.479, C:A.480, C:A.481, C:D.495 Salt bridges: C:K.51 ADP.13: 23 residues within 4Å: Chain D: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.14, MG.15, K.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.30, D:G.32, D:G.88, D:T.90, D:T.90, D:T.91, D:G.415, D:G.416, D:N.479, D:A.480, D:A.481, D:D.495 Salt bridges: D:K.51 ADP.17: 22 residues within 4Å: Chain E: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.18, MG.19, K.20 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:T.30, E:T.30, E:G.32, E:G.88, E:T.90, E:T.90, E:T.91, E:T.91, E:G.415, E:G.416, E:N.479, E:A.480, E:A.481, E:D.495 Salt bridges: E:K.51 ADP.21: 22 residues within 4Å: Chain F: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.22, MG.23, K.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.32, F:G.88, F:G.88, F:T.90, F:T.90, F:T.91, F:T.91, F:G.415, F:G.416, F:N.479, F:A.480, F:A.481, F:D.495 Salt bridges: F:K.51 ADP.25: 22 residues within 4Å: Chain G: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.26, MG.27, K.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:T.30, G:G.32, G:G.88, G:G.88, G:T.89, G:T.90, G:T.90, G:T.91, G:T.91, G:G.415, G:N.479, G:A.480, G:A.481, G:D.495 Salt bridges: G:K.51 ADP.29: 22 residues within 4Å: Chain O: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.30, MG.31, K.32 15 PLIP interactions: 15 interactions with chain O Hydrogen bonds: O:T.30, O:G.32, O:G.88, O:G.88, O:T.89, O:T.90, O:T.90, O:T.91, O:T.91, O:G.415, O:N.479, O:A.480, O:A.481, O:D.495 Salt bridges: O:K.51 ADP.33: 22 residues within 4Å: Chain P: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.34, MG.35, K.36 14 PLIP interactions: 14 interactions with chain P Hydrogen bonds: P:T.30, P:G.32, P:G.88, P:G.88, P:T.90, P:T.90, P:T.91, P:T.91, P:G.415, P:N.479, P:A.480, P:A.481, P:D.495 Salt bridges: P:K.51 ADP.37: 21 residues within 4Å: Chain Q: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, D.495 Ligands: BEF.38, MG.39, K.40 13 PLIP interactions: 13 interactions with chain Q Hydrogen bonds: Q:T.30, Q:G.32, Q:G.88, Q:G.88, Q:T.90, Q:T.91, Q:T.91, Q:G.415, Q:N.479, Q:A.480, Q:A.481, Q:D.495 Salt bridges: Q:K.51 ADP.41: 22 residues within 4Å: Chain R: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.42, MG.43, K.44 14 PLIP interactions: 14 interactions with chain R Hydrogen bonds: R:T.30, R:G.32, R:G.88, R:G.88, R:T.89, R:T.89, R:T.90, R:T.91, R:G.415, R:N.479, R:A.480, R:A.481, R:D.495 Salt bridges: R:K.51 ADP.45: 22 residues within 4Å: Chain S: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.46, MG.47, K.48 16 PLIP interactions: 16 interactions with chain S Hydrogen bonds: S:G.32, S:G.88, S:T.89, S:T.89, S:T.90, S:T.90, S:T.90, S:T.91, S:T.91, S:T.91, S:G.415, S:N.479, S:A.480, S:A.481, S:D.495 Salt bridges: S:K.51 ADP.49: 22 residues within 4Å: Chain T: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.50, MG.51, K.52 14 PLIP interactions: 14 interactions with chain T Hydrogen bonds: T:G.32, T:G.88, T:G.88, T:G.88, T:T.90, T:T.90, T:T.91, T:T.91, T:G.415, T:N.479, T:A.480, T:A.481, T:D.495 Salt bridges: T:K.51 ADP.53: 23 residues within 4Å: Chain U: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.54, MG.55, K.56 16 PLIP interactions: 16 interactions with chain U Hydrogen bonds: U:T.30, U:G.32, U:G.88, U:G.88, U:T.89, U:T.90, U:T.90, U:T.91, U:T.91, U:G.415, U:G.416, U:N.479, U:A.480, U:A.481, U:D.495 Salt bridges: U:K.51

14 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 11 residues within 4Å: Chain A: D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.1, MG.3, K.4 No protein-ligand interaction detected (PLIP) BEF.6: 10 residues within 4Å: Chain B: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.5, MG.7, K.8 No protein-ligand interaction detected (PLIP) BEF.10: 11 residues within 4Å: Chain C: T.30, K.51, D.52, G.53, D.87, T.89, T.90, D.398 Ligands: ADP.9, MG.11, K.12 No protein-ligand interaction detected (PLIP) BEF.14: 11 residues within 4Å: Chain D: D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.13, MG.15, K.16 No protein-ligand interaction detected (PLIP) BEF.18: 11 residues within 4Å: Chain E: D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.17, MG.19, K.20 No protein-ligand interaction detected (PLIP) BEF.22: 11 residues within 4Å: Chain F: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.21, MG.23, K.24 No protein-ligand interaction detected (PLIP) BEF.26: 11 residues within 4Å: Chain G: D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.25, MG.27, K.28 No protein-ligand interaction detected (PLIP) BEF.30: 11 residues within 4Å: Chain O: D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.29, MG.31, K.32 No protein-ligand interaction detected (PLIP) BEF.34: 11 residues within 4Å: Chain P: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.33, MG.35, K.36 No protein-ligand interaction detected (PLIP) BEF.38: 10 residues within 4Å: Chain Q: D.52, G.53, G.86, D.87, T.89, T.90, D.398 Ligands: ADP.37, MG.39, K.40 No protein-ligand interaction detected (PLIP) BEF.42: 11 residues within 4Å: Chain R: K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.41, MG.43, K.44 No protein-ligand interaction detected (PLIP) BEF.46: 11 residues within 4Å: Chain S: D.52, G.53, G.86, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.45, MG.47, K.48 No protein-ligand interaction detected (PLIP) BEF.50: 11 residues within 4Å: Chain T: T.30, K.51, D.52, G.53, D.87, G.88, T.89, T.90 Ligands: ADP.49, MG.51, K.52 No protein-ligand interaction detected (PLIP) BEF.54: 12 residues within 4Å: Chain U: T.30, K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.53, MG.55, K.56 No protein-ligand interaction detected (PLIP)

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.87 Ligands: ADP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.7: 3 residues within 4Å: Chain B: D.87 Ligands: ADP.5, BEF.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.87, B:D.87 MG.11: 5 residues within 4Å: Chain C: D.87, S.151 Ligands: ADP.9, BEF.10, K.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.87, C:D.87 MG.15: 4 residues within 4Å: Chain D: D.87, S.151 Ligands: ADP.13, BEF.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.87, D:D.87 MG.19: 4 residues within 4Å: Chain E: D.87, S.151 Ligands: ADP.17, BEF.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.87, E:D.87 MG.23: 4 residues within 4Å: Chain F: D.87, S.151 Ligands: ADP.21, BEF.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.87, F:D.87 MG.27: 4 residues within 4Å: Chain G: D.87, S.151 Ligands: ADP.25, BEF.26 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.87, G:D.87 MG.31: 3 residues within 4Å: Chain O: D.87 Ligands: ADP.29, BEF.30 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.87, O:D.87 MG.35: 4 residues within 4Å: Chain P: D.87, S.151 Ligands: ADP.33, BEF.34 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.87, P:D.87 MG.39: 4 residues within 4Å: Chain Q: D.87, S.151 Ligands: ADP.37, BEF.38 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.87 MG.43: 4 residues within 4Å: Chain R: D.87, S.151 Ligands: ADP.41, BEF.42 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:D.87, R:D.87 MG.47: 4 residues within 4Å: Chain S: D.87, S.151 Ligands: ADP.45, BEF.46 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:D.87, S:D.87 MG.51: 4 residues within 4Å: Chain T: D.87, S.151 Ligands: ADP.49, BEF.50 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:D.87, T:D.87 MG.55: 4 residues within 4Å: Chain U: D.87, S.151 Ligands: ADP.53, BEF.54 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:D.87, U:D.87

14 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: T.30, K.51, G.53, T.90 Ligands: ADP.1, BEF.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.30, A:K.51, A:T.90 K.8: 5 residues within 4Å: Chain B: T.30, K.51, T.90 Ligands: ADP.5, BEF.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.30, B:K.51, B:T.90 K.12: 4 residues within 4Å: Chain C: K.51 Ligands: ADP.9, BEF.10, MG.11 No protein-ligand interaction detected (PLIP) K.16: 6 residues within 4Å: Chain D: T.30, K.51, G.53, T.90 Ligands: ADP.13, BEF.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:K.51, D:T.90 K.20: 5 residues within 4Å: Chain E: T.30, K.51, T.90 Ligands: ADP.17, BEF.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:K.51 K.24: 5 residues within 4Å: Chain F: T.30, K.51, T.90 Ligands: ADP.21, BEF.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:K.51, F:T.90 K.28: 5 residues within 4Å: Chain G: T.30, K.51, T.90 Ligands: ADP.25, BEF.26 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:K.51 K.32: 6 residues within 4Å: Chain O: T.30, K.51, G.53, T.90 Ligands: ADP.29, BEF.30 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:T.30, O:K.51, O:T.90 K.36: 5 residues within 4Å: Chain P: T.30, K.51, T.90 Ligands: ADP.33, BEF.34 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:T.30, P:T.30 K.40: 6 residues within 4Å: Chain Q: T.30, K.51, G.53, T.90 Ligands: ADP.37, BEF.38 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:K.51, Q:T.90 K.44: 5 residues within 4Å: Chain R: T.30, K.51, T.90 Ligands: ADP.41, BEF.42 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.90 K.48: 5 residues within 4Å: Chain S: T.30, K.51, T.90 Ligands: ADP.45, BEF.46 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:K.51, S:T.90 K.52: 4 residues within 4Å: Chain T: T.30, K.51 Ligands: ADP.49, BEF.50 No protein-ligand interaction detected (PLIP) K.56: 4 residues within 4Å: Chain U: T.30, K.51 Ligands: ADP.53, BEF.54 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:T.30, U:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fei, X. et al., Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-08-20

Peptides

60 kDa chaperonin: ABCDEFGOPQRSTU
10 kDa chaperonin: HIJKLMNVWXYZ01

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

C
B

D
F

E
E

F
C

G
D

O
K

P
J

Q
I

R
L

S
M

T
H

U
N

H
O

I
P

J
Q

K
U

L
T

M
R

N
S

V
X

W
W

X
V

Y
Y

Z
Z

0
2

1
1

60 kDa chaperonin

10 kDa chaperonin

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