SMTL ID : 1svt.1

Crystal structure of GroEL14-GroES7-(ADP-AlFx)7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-14-7-mer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.86 Ligands: ADP.3, AF3.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 MG.5: 3 residues within 4Å: Chain B: D.86 Ligands: ADP.7, AF3.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.86 MG.9: 3 residues within 4Å: Chain C: D.86 Ligands: ADP.11, AF3.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.13: 3 residues within 4Å: Chain D: D.86 Ligands: ADP.15, AF3.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.17: 3 residues within 4Å: Chain E: D.86 Ligands: ADP.19, AF3.20 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.86, H2O.3 MG.21: 3 residues within 4Å: Chain F: D.86 Ligands: ADP.23, AF3.24 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.25: 3 residues within 4Å: Chain G: D.86 Ligands: ADP.27, AF3.28 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86

7 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: T.29, K.50, T.89 Ligands: ADP.3, AF3.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.29, A:K.50, A:T.89 K.6: 5 residues within 4Å: Chain B: T.29, K.50, T.89 Ligands: ADP.7, AF3.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:K.50 K.10: 6 residues within 4Å: Chain C: T.29, L.30, K.50, T.89 Ligands: ADP.11, AF3.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.29, C:T.29, C:K.50 K.14: 5 residues within 4Å: Chain D: T.29, K.50, T.89 Ligands: ADP.15, AF3.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:K.50, D:T.89 K.18: 5 residues within 4Å: Chain E: T.29, K.50, T.89 Ligands: ADP.19, AF3.20 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.29, E:K.50 K.22: 5 residues within 4Å: Chain F: T.29, K.50, T.89 Ligands: ADP.23, AF3.24 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:K.50 K.26: 5 residues within 4Å: Chain G: T.29, K.50, T.89 Ligands: ADP.27, AF3.28 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.29, G:K.50, G:T.89

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

ADP.3: 25 residues within 4Å: Chain A: T.29, 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.1, K.2, AF3.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.31, A:G.87, A:G.87, A:T.89, A:T.89, A:T.90, A:G.414, A:G.415, A:N.478, A:A.479, A:A.480, A:D.494 Salt bridges: A:K.50 ADP.7: 24 residues within 4Å: Chain B: T.29, 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, I.492, D.494 Ligands: MG.5, K.6, AF3.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.31, B:G.87, B:G.87, B:T.89, B:T.89, B:T.90, B:G.414, B:G.415, B:N.478, B:A.479, B:A.480, B:D.494 Salt bridges: B:K.50 ADP.11: 24 residues within 4Å: Chain C: T.29, 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, I.492, D.494 Ligands: MG.9, K.10, AF3.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.31, C:G.87, C:G.87, C:T.89, C:T.89, C:T.90, C:G.414, C:G.415, C:N.478, C:A.479, C:A.480, C:D.494 Salt bridges: C:K.50 ADP.15: 24 residues within 4Å: Chain D: T.29, 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, I.492, D.494 Ligands: MG.13, K.14, AF3.16 14 PLIP interactions: 14 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:G.414, D:G.415, D:N.478, D:A.479, D:A.480, D:D.494 Salt bridges: D:K.50 ADP.19: 25 residues within 4Å: Chain E: T.29, 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.17, K.18, AF3.20 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.31, E:G.87, E:G.87, E:T.89, E:T.89, E:T.90, E:G.414, E:G.415, E:N.478, E:A.479, E:A.480, E:D.494 Water bridges: E:D.397 Salt bridges: E:K.50 ADP.23: 24 residues within 4Å: Chain F: T.29, 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, I.492, D.494 Ligands: MG.21, K.22, AF3.24 14 PLIP interactions: 14 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:G.414, F:G.415, F:N.478, F:A.479, F:A.480, F:D.494 Salt bridges: F:K.50 ADP.27: 24 residues within 4Å: Chain G: T.29, 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, I.492, D.494 Ligands: MG.25, K.26, AF3.28 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:G.31, G:G.87, G:G.87, G:T.89, G:T.89, G:T.90, G:G.414, G:G.415, G:N.478, G:A.479, G:A.480, G:D.494 Salt bridges: G:K.50

7 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.4: 9 residues within 4Å: Chain A: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: MG.1, K.2, ADP.3 No protein-ligand interaction detected (PLIP) AF3.8: 9 residues within 4Å: Chain B: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: MG.5, K.6, ADP.7 No protein-ligand interaction detected (PLIP) AF3.12: 11 residues within 4Å: Chain C: K.50, D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.9, K.10, ADP.11 No protein-ligand interaction detected (PLIP) AF3.16: 9 residues within 4Å: Chain D: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: MG.13, K.14, ADP.15 No protein-ligand interaction detected (PLIP) AF3.20: 10 residues within 4Å: Chain E: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.17, K.18, ADP.19 No protein-ligand interaction detected (PLIP) AF3.24: 9 residues within 4Å: Chain F: D.51, G.52, D.86, G.87, T.88, T.89 Ligands: MG.21, K.22, ADP.23 No protein-ligand interaction detected (PLIP) AF3.28: 10 residues within 4Å: Chain G: D.51, G.52, D.86, G.87, T.88, T.89, D.397 Ligands: MG.25, K.26, ADP.27 No protein-ligand interaction detected (PLIP)

Links

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Citation

Chaudhry, C. et al., Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J.Mol.Biol. (2004)

Release Date

2005-03-01

Peptides

groEL protein: ABCDEFGHIJKLMN
groES protein: OPQRSTU

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

groEL protein

groES protein

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