SMTL ID : 4v81.2 (1 other biounit)

The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: S.43, L.44, G.45, P.46, N.64, D.96, G.97, T.99, S.100, T.162, S.165, S.166, G.422, L.462, L.502, V.517 Ligands: BEF.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.45, A:N.64, A:D.96, A:G.97, A:T.99, A:S.100, A:T.162, A:S.165, A:S.165, A:S.165, A:S.166, A:S.166, A:G.422 ADP.3: 18 residues within 4Å: Chain B: T.36, L.37, G.38, N.58, D.90, G.91, T.93, S.94, T.159, S.162, S.163, G.403, G.404, L.444, L.474, I.487, E.489 Ligands: BEF.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.38, B:N.58, B:N.58, B:G.91, B:G.91, B:T.93, B:S.94, B:S.162, B:S.162, B:S.163, B:S.163, B:G.404, B:E.489, B:E.489 ADP.7: 17 residues within 4Å: Chain E: G.66, P.67, N.85, D.117, G.118, T.120, G.121, T.186, S.190, D.425, G.443, L.483, V.512, D.513, C.514, V.527 Ligands: BEF.8 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.66, E:N.85, E:G.118, E:T.120, E:T.120, E:G.121, E:T.186, E:S.190, E:G.443, E:D.513, E:D.513, E:C.514 ADP.9: 18 residues within 4Å: Chain F: N.36, L.37, G.38, P.39, K.57, D.89, G.90, T.92, T.93, S.156, A.415, Y.419, L.458, V.491, L.493, N.494, D.508 Ligands: BEF.10 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.38, F:G.90, F:T.92, F:T.93, F:T.93, F:T.93, F:Y.419, F:L.493, F:N.494 Salt bridges: F:K.57 ADP.11: 15 residues within 4Å: Chain G: T.43, L.44, G.45, P.46, N.64, D.96, G.97, T.98, T.99, S.100, S.168, G.413, F.483, E.498 Ligands: BEF.12 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.45, G:D.96, G:T.98, G:T.99, G:T.99, G:S.100, G:S.168, G:S.168, G:S.168, G:G.413 ADP.13: 18 residues within 4Å: Chain H: M.46, G.47, P.48, N.66, D.98, G.99, T.100, N.101, L.102, S.168, S.169, A.423, G.424, L.463, K.491, H.494, D.506 Ligands: BEF.14 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:G.47, H:N.66, H:D.98, H:G.99, H:G.99, H:T.100, H:N.101, H:N.101, H:L.102, H:S.169, H:A.423, H:G.424, H:H.494 ADP.17: 15 residues within 4Å: Chain K: L.39, G.40, N.59, D.91, T.94, T.95, Q.156, A.157, T.161, G.471, G.472, G.473, L.512, E.557 Ligands: BEF.18 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:G.40, K:N.59, K:A.157, K:T.161, K:G.472, K:G.473, K:E.557 ADP.19: 17 residues within 4Å: Chain L: S.38, L.39, G.40, P.41, D.91, T.94, T.156, S.160, K.161, G.413, G.414, G.415, I.450, L.454, R.485, Q.499 Ligands: BEF.20 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.40, L:D.91, L:S.160, L:G.414, L:G.415, L:R.485, L:R.485, L:Q.499, L:Q.499 Salt bridges: L:K.161 ADP.21: 19 residues within 4Å: Chain M: S.64, L.65, G.66, P.67, N.85, D.117, G.118, T.120, G.121, T.186, G.444, I.479, L.483, V.512, D.513, C.514, V.527, D.529 Ligands: BEF.22 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:G.66, M:N.85, M:N.85, M:G.118, M:T.120, M:G.121, M:T.186, M:G.444, M:D.513, M:C.514 ADP.23: 19 residues within 4Å: Chain N: N.36, L.37, G.38, P.39, K.57, D.89, G.90, T.92, T.93, S.156, L.159, A.415, G.416, Y.419, V.491, N.494, I.506, D.508 Ligands: BEF.24 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:G.38, N:G.90, N:T.92, N:T.93, N:T.93, N:T.93, N:A.415, N:G.416, N:Y.419, N:N.494 Salt bridges: N:K.57 ADP.26: 17 residues within 4Å: Chain P: G.47, P.48, D.98, G.99, T.100, N.101, L.102, P.165, S.168, S.169, G.422, A.423, G.424, E.427, L.463, D.506 Ligands: BEF.27 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:G.47, P:D.98, P:D.98, P:G.99, P:T.100, P:T.100, P:N.101, P:N.101, P:L.102, P:S.168, P:S.169, P:A.423, P:G.424

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

BEF.2: 9 residues within 4Å: Chain A: D.65, G.66, G.95, D.96, G.97, T.98, T.99, D.404 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) BEF.4: 10 residues within 4Å: Chain B: N.58, D.59, G.60, G.89, D.90, G.91, T.92, T.93, D.386 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) BEF.8: 10 residues within 4Å: Chain E: N.85, D.86, G.87, G.116, D.117, G.118, T.119, T.120, D.425 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) BEF.10: 5 residues within 4Å: Chain F: K.57, D.58, D.89, D.397 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) BEF.12: 7 residues within 4Å: Chain G: D.65, D.96, T.98, A.165, S.168, D.395 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) BEF.14: 6 residues within 4Å: Chain H: D.98, G.99, T.100, N.101, D.403 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) BEF.18: 7 residues within 4Å: Chain K: D.91, G.92, T.93, T.94, T.95, D.454 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) BEF.20: 6 residues within 4Å: Chain L: D.91, G.92, T.93, T.94, S.95 Ligands: ADP.19 No protein-ligand interaction detected (PLIP) BEF.22: 6 residues within 4Å: Chain M: N.85, D.86, D.117, G.118, D.425 Ligands: ADP.21 No protein-ligand interaction detected (PLIP) BEF.24: 4 residues within 4Å: Chain N: K.57, D.89, S.157 Ligands: ADP.23 No protein-ligand interaction detected (PLIP) BEF.27: 7 residues within 4Å: Chain P: N.66, D.67, D.98, T.100, N.101, D.403 Ligands: ADP.26 No protein-ligand interaction detected (PLIP)

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain C: D.91, G.92, T.93, T.94 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.91, C:G.92, C:T.94, C:T.94 SO4.6: 5 residues within 4Å: Chain D: D.91, G.92, T.93, T.94, S.95 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.92, D:T.93, D:T.93, D:T.94, D:S.95 SO4.15: 5 residues within 4Å: Chain I: L.44, D.96, G.97, T.99, S.166 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:G.97, I:T.99, I:T.99, I:S.166 SO4.16: 5 residues within 4Å: Chain J: T.36, D.90, G.91, T.93, S.94 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:T.36, J:D.90, J:G.91 SO4.25: 3 residues within 4Å: Chain O: D.96, T.98, T.99 3 PLIP interactions: 3 interactions with chain O Hydrogen bonds: O:T.98, O:T.99, O:T.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dekker, C. et al., The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins. Embo J. (2011)

Release Date

2014-07-09

Peptides

T-complex protein 1 subunit alpha: AI
T-complex protein 1 subunit beta: BJ
T-complex protein 1 subunit gamma: CK
T-complex protein 1 subunit delta: DL
T-complex protein 1 subunit epsilon: EM
T-complex protein 1 subunit zeta: FN
T-complex protein 1 subunit eta: GO
T-complex protein 1 subunit theta: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

I
i

B
b

J
j

C
c

K
k

D
d

L
l

E
e

M
m

F
f

N
n

G
g

O
o

H
h

P
p

T-complex protein 1 subunit alpha

T-complex protein 1 subunit beta

T-complex protein 1 subunit gamma

T-complex protein 1 subunit delta

T-complex protein 1 subunit epsilon

T-complex protein 1 subunit zeta

T-complex protein 1 subunit eta

T-complex protein 1 subunit theta

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