SMTL ID : 4pko.1

Crystal structure of the Football-shaped GroEL-GroES2-(ADPBeFx)14 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.84 Å

Oligo State

hetero-14-14-mer

Ligands

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

ADP.1: 24 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, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.2, MG.3, K.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.30, A:G.32, A:G.88, A:G.88, A:T.90, A:T.91, A:T.91, A:T.91, A:G.415, A:G.416, A:N.479, 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, G.416, I.454, Y.478, N.479, A.480, A.481, D.495 Ligands: BEF.6, MG.7, K.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.32, B:G.88, B:T.89, B:T.90, B:T.90, B:T.91, B:T.91, B:T.91, B:G.415, B:G.416, B:N.479, B:A.480, B:A.481, B:D.495 Salt bridges: B:K.51 ADP.9: 22 residues within 4Å: Chain C: T.30, L.31, G.32, P.33, K.51, D.87, T.89, T.90, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.10, MG.11, K.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:T.30, C:G.32, C:T.89, C:T.90, C:T.90, C:G.415, C:G.416, C:N.479, C:A.480, C:A.481, C:D.495 Salt bridges: C:K.51, 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 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.30, D:G.32, D:G.88, D:G.88, D:T.90, D:T.90, D:T.91, D:T.91, 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: 23 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, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.18, MG.19, K.20 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:T.30, E:G.32, E:G.88, E:T.89, E:T.90, E:T.90, E:T.91, 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: L.31, G.32, P.33, D.87, G.88, T.89, T.90, T.91, S.154, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.22, MG.23, K.24 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.32, F:G.88, F:T.89, F:T.89, F:T.90, F:T.90, F:T.91, F:S.154, F:S.154, F:G.415, F:G.416, F:A.480, F:A.481, F:D.495 Salt bridges: F:K.51 ADP.25: 23 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, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.26, MG.27, K.28 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:G.32, G:G.88, G:G.88, G:T.89, G:T.89, G:T.90, G:T.90, G:T.90, G:T.91, G:G.415, G:G.416, G:N.479, G:A.480, G:A.481, G:D.495 Salt bridges: G:K.51 ADP.29: 24 residues within 4Å: Chain H: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, S.151, G.414, G.415, G.416, 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 H Hydrogen bonds: H:T.30, H:G.32, H:G.88, H:G.88, H:T.90, H:T.90, H:T.90, H:T.91, H:G.415, H:G.416, H:N.479, H:A.480, H:A.481, H:D.495 Salt bridges: H:K.51 ADP.33: 24 residues within 4Å: Chain I: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, 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 I Hydrogen bonds: I:G.32, I:G.88, I:T.89, I:T.90, I:T.91, I:T.91, I:T.91, I:G.415, I:G.416, I:N.479, I:A.480, I:A.481, I:D.495 Salt bridges: I:K.51 ADP.37: 22 residues within 4Å: Chain J: 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.38, MG.39, K.40 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:T.30, J:T.30, J:G.32, J:G.88, J:T.89, J:T.89, J:T.90, J:T.91, J:G.415, J:G.416, J:N.479, J:A.480, J:A.481, J:D.495 Salt bridges: J:K.51 ADP.41: 23 residues within 4Å: Chain K: 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.42, MG.43, K.44 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:T.30, K:G.32, K:G.88, K:G.88, K:T.89, K:T.90, K:T.90, K:T.91, K:T.91, K:G.415, K:G.416, K:N.479, K:A.480, K:A.481, K:D.495 Salt bridges: K:K.51 ADP.45: 24 residues within 4Å: Chain L: T.30, L.31, G.32, P.33, K.51, D.87, G.88, T.89, T.90, T.91, I.150, G.414, G.415, G.416, I.454, Y.478, N.479, A.480, A.481, I.493, D.495 Ligands: BEF.46, MG.47, K.48 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:G.32, L:G.88, L:T.89, L:T.90, L:T.90, L:T.90, L:T.91, L:T.91, L:S.154, L:S.154, L:G.415, L:G.416, L:N.479, L:A.480, L:A.481, L:D.495 Salt bridges: L:K.51 ADP.49: 23 residues within 4Å: Chain M: 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.50, MG.51, K.52 16 PLIP interactions: 16 interactions with chain M Hydrogen bonds: M:T.30, M:G.32, M:G.88, M:G.88, M:T.90, M:T.90, M:T.91, M:T.91, M:T.91, M:G.415, M:G.416, M:N.479, M:A.480, M:A.481, M:D.495 Salt bridges: M:K.51 ADP.53: 23 residues within 4Å: Chain N: 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 14 PLIP interactions: 14 interactions with chain N Hydrogen bonds: N:G.32, N:G.88, N:G.88, N:T.89, N:T.90, N:T.91, N:G.415, N:G.416, N:N.479, N:N.479, N:A.480, N:A.481, N:D.495 Salt bridges: N:K.51

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

BEF.2: 12 residues within 4Å: Chain A: K.51, 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: 9 residues within 4Å: Chain B: D.52, 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: 7 residues within 4Å: Chain C: D.87, G.88, T.89, T.90, T.91 Ligands: ADP.9, MG.11 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: T.30, K.51, D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.21, MG.23 No protein-ligand interaction detected (PLIP) BEF.26: 11 residues within 4Å: Chain G: K.51, D.52, G.53, 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 H: D.52, G.53, V.54, 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 I: D.52, G.53, D.87, G.88, T.89, T.90, T.91, D.398 Ligands: ADP.33, MG.35, K.36 No protein-ligand interaction detected (PLIP) BEF.38: 12 residues within 4Å: Chain J: K.51, D.52, G.53, G.86, D.87, G.88, 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 K: K.51, D.52, G.53, G.86, D.87, T.89, T.90, D.398 Ligands: ADP.41, MG.43, K.44 No protein-ligand interaction detected (PLIP) BEF.46: 12 residues within 4Å: Chain L: K.51, 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: 10 residues within 4Å: Chain M: D.52, G.53, D.87, G.88, T.89, T.90, D.398 Ligands: ADP.49, MG.51, K.52 No protein-ligand interaction detected (PLIP) BEF.54: 11 residues within 4Å: Chain N: 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: 4 residues within 4Å: Chain A: D.87, G.88 Ligands: ADP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:D.87 MG.7: 4 residues within 4Å: Chain B: D.87, S.151 Ligands: ADP.5, BEF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.87 MG.11: 4 residues within 4Å: Chain C: D.87, S.151 Ligands: ADP.9, BEF.10 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 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.87 MG.23: 3 residues within 4Å: Chain F: D.87 Ligands: ADP.21, BEF.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.87 MG.27: 4 residues within 4Å: Chain G: D.87, S.151 Ligands: ADP.25, BEF.26 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.87 MG.31: 3 residues within 4Å: Chain H: D.87 Ligands: ADP.29, BEF.30 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.87, H:D.87 MG.35: 6 residues within 4Å: Chain I: D.87, S.151, D.398 Ligands: ADP.33, BEF.34, K.36 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.87 MG.39: 5 residues within 4Å: Chain J: D.87, S.151, D.398 Ligands: ADP.37, BEF.38 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.87, J:D.87 MG.43: 4 residues within 4Å: Chain K: D.87, D.398 Ligands: ADP.41, BEF.42 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.87 MG.47: 4 residues within 4Å: Chain L: D.87, S.151 Ligands: ADP.45, BEF.46 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.87 MG.51: 3 residues within 4Å: Chain M: D.87 Ligands: ADP.49, BEF.50 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.87 MG.55: 3 residues within 4Å: Chain N: D.87 Ligands: ADP.53, BEF.54 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.87, N: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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.30, A:T.30, A:K.51, A:T.90 K.8: 6 residues within 4Å: Chain B: T.30, K.51, G.53, T.90 Ligands: ADP.5, BEF.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:K.51, B:T.90 K.12: 5 residues within 4Å: Chain C: T.30, K.51, G.53, T.90 Ligands: ADP.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.30, C:K.51, C:T.90 K.16: 5 residues within 4Å: Chain D: T.30, K.51, 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, L.31, G.32, K.51 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.30 K.28: 6 residues within 4Å: Chain G: T.30, K.51, G.53, T.90 Ligands: ADP.25, BEF.26 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.30, G:T.30, G:K.51 K.32: 6 residues within 4Å: Chain H: T.30, K.51, G.53, T.90 Ligands: ADP.29, BEF.30 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.30, H:K.51 K.36: 7 residues within 4Å: Chain I: T.30, K.51, G.53, T.90 Ligands: ADP.33, BEF.34, MG.35 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:K.51 K.40: 5 residues within 4Å: Chain J: T.30, K.51, T.90 Ligands: ADP.37, BEF.38 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:K.51 K.44: 5 residues within 4Å: Chain K: T.30, K.51, T.90 Ligands: ADP.41, BEF.42 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:T.30, K:K.51 K.48: 6 residues within 4Å: Chain L: T.30, K.51, G.53, T.90 Ligands: ADP.45, BEF.46 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:K.51, L:T.90 K.52: 6 residues within 4Å: Chain M: T.30, K.51, G.53, T.90 Ligands: ADP.49, BEF.50 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:T.30, M:K.51, M:T.90 K.56: 5 residues within 4Å: Chain N: T.30, K.51, T.90 Ligands: ADP.53, BEF.54 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:K.51, N:T.90

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: ABCDEFGHIJKLMN
10 kDa chaperonin: OPQRSTUVWXYZ01

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
V

W
W

X
X

Y
Y

Z
Z

0
1

1
2

60 kDa chaperonin

10 kDa chaperonin

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