SMTL ID : 4v4o.2 (1 other biounit)

Crystal Structure of the Chaperonin Complex Cpn60/Cpn10/(ADP)7 from Thermus Thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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, S.150 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 MG.3: 3 residues within 4Å: Chain B: D.86, S.150 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.86 MG.5: 3 residues within 4Å: Chain C: D.86, S.150 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.7: 4 residues within 4Å: Chain D: D.86, S.150, D.396 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86 MG.9: 3 residues within 4Å: Chain E: D.86, S.150 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.86, E:S.150 MG.11: 4 residues within 4Å: Chain F: D.86, S.150, D.396 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.86 MG.13: 3 residues within 4Å: Chain G: D.86, S.150 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.86

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

ADP.2: 23 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.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, M.489, I.494, D.496 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.31, A:G.87, A:G.87, A:T.88, A:T.88, A:T.88, A:T.89, A:T.89, A:T.90, A:G.413, A:G.414, A:N.480, A:A.481, A:A.482, A:D.496 Salt bridges: A:K.50 ADP.4: 23 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.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, M.489, I.494, D.496 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.31, B:G.87, B:G.87, B:T.88, B:T.88, B:T.88, B:T.89, B:T.89, B:T.90, B:G.413, B:G.414, B:N.480, B:A.481, B:A.482, B:D.496 Salt bridges: B:K.50 ADP.6: 23 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.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, M.489, I.494, D.496 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.31, C:G.87, C:G.87, C:T.88, C:T.88, C:T.88, C:T.89, C:T.89, C:T.90, C:T.90, C:G.413, C:G.414, C:N.480, C:A.481, C:A.482, C:D.496 Salt bridges: C:K.50 ADP.8: 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, N.152, G.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, M.489, I.494, D.496 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.31, D:G.87, D:G.87, D:T.88, D:T.88, D:T.88, D:T.89, D:T.89, D:T.90, D:T.90, D:G.413, D:G.414, D:N.480, D:A.481, D:D.496 Salt bridges: D:K.50 ADP.10: 23 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.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, M.489, I.494, D.496 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:G.31, E:G.87, E:G.87, E:T.88, E:T.88, E:T.88, E:T.89, E:T.89, E:T.90, E:T.90, E:G.413, E:G.414, E:N.480, E:A.481, E:D.496 Salt bridges: E:K.50 ADP.12: 23 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, N.152, G.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, I.494, D.496 Ligands: MG.11 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:G.31, F:G.87, F:G.87, F:T.88, F:T.88, F:T.88, F:T.89, F:T.89, F:T.90, F:T.90, F:G.413, F:G.414, F:N.480, F:A.481, F:A.482, F:D.496 Salt bridges: F:K.50 ADP.14: 23 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.412, G.413, G.414, I.453, F.479, N.480, A.481, A.482, M.489, I.494, D.496 Ligands: MG.13 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:G.31, G:G.87, G:G.87, G:T.88, G:T.88, G:T.88, G:T.89, G:T.89, G:T.90, G:T.90, G:G.413, G:G.414, G:N.480, G:A.481, G:A.482, G:D.496 Salt bridges: G:K.50

7 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.15: 6 residues within 4Å: Chain A: A.107, A.108 Chain H: E.101, K.104, N.105, K.440 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:E.101, H:K.104, H:N.105 Salt bridges: H:E.101 DMS.16: 5 residues within 4Å: Chain B: A.107, A.108 Chain I: E.101, K.104, N.105 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:K.104, I:N.105 Salt bridges: I:E.101 DMS.17: 7 residues within 4Å: Chain C: A.107, A.108, G.109 Chain J: E.101, K.104, N.105, K.440 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:K.104, J:N.105 Salt bridges: J:E.101 DMS.18: 4 residues within 4Å: Chain D: A.107 Chain K: E.101, K.104, N.105 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:E.101, K:K.104, K:N.105 Salt bridges: K:E.101 DMS.19: 5 residues within 4Å: Chain E: A.107, A.108 Chain L: E.101, K.104, N.105 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:E.101, L:K.104, L:N.105 Salt bridges: L:E.101 DMS.20: 5 residues within 4Å: Chain F: A.107, A.108 Chain M: E.101, K.104, N.105 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:E.101, M:K.104, M:N.105 Salt bridges: M:E.101 DMS.21: 5 residues within 4Å: Chain G: A.107, A.108 Chain N: E.101, K.104, N.105 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:E.101, N:K.104, N:N.105 Salt bridges: N:E.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimamura, T. et al., Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity. STRUCTURE (2004)

Release Date

2014-07-09

Peptides

cpn60(GroEL): ABCDEFGHIJKLMN
cpn10(GroES): 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

cpn60(GroEL)

cpn10(GroES)

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