SMTL ID : 4v8r.2 (1 other biounit)

The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

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

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: S.43, L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.162, S.165, S.166, G.421, G.422, I.458, L.462, L.502, E.512, V.517, E.519, K.524 Ligands: BEF.2, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.43, A:G.45, A:G.97, A:G.97, A:T.99, A:S.100, A:S.165, A:S.165, A:S.165, A:S.166, A:G.422, A:E.519, A:K.524 ADP.4: 22 residues within 4Å: Chain B: T.36, L.37, G.38, P.39, N.58, D.90, G.91, T.92, T.93, S.94, T.159, S.162, S.163, G.403, G.404, L.444, L.472, I.487, E.489, K.494 Ligands: BEF.5, MG.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.38, B:N.58, B:G.91, B:G.91, B:T.93, B:T.93, B:S.94, B:S.162, B:S.163, B:G.404, B:G.405, B:E.489, B:K.494 Salt bridges: B:K.164, B:K.164 ADP.7: 25 residues within 4Å: Chain C: S.38, L.39, G.40, P.41, N.59, D.91, G.92, T.93, T.94, S.95, T.156, S.159, S.160, K.161, G.414, G.415, L.454, I.482, S.483, V.484, R.485, I.497, Q.499 Ligands: BEF.8, MG.9 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.40, C:N.59, C:G.92, C:G.92, C:T.94, C:T.94, C:S.95, C:S.95, C:S.95, C:S.159, C:S.159, C:S.160, C:G.414, C:G.415, C:V.484, C:R.485, C:Q.499 Salt bridges: C:K.161, C:K.161 ADP.10: 20 residues within 4Å: Chain D: S.64, L.65, G.66, P.67, N.85, D.117, G.118, T.119, T.120, G.121, T.186, S.190, G.443, G.444, L.483, C.514, V.527, D.529 Ligands: BEF.11, MG.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.64, D:G.66, D:N.85, D:G.118, D:T.120, D:T.120, D:G.121, D:S.190, D:G.443, D:G.444, D:D.529 ADP.13: 21 residues within 4Å: Chain E: C.38, L.39, G.40, D.91, G.92, T.93, T.94, T.95, T.161, G.471, G.472, G.473, E.476, L.512, I.540, G.542, Y.553, I.555, E.557 Ligands: BEF.14, MG.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:C.38, E:G.40, E:G.92, E:G.92, E:T.93, E:T.94, E:T.95, E:G.472, E:G.473, E:E.476, E:G.542, E:Y.553, E:E.557 ADP.16: 21 residues within 4Å: Chain F: T.43, L.44, G.45, N.64, D.96, G.97, T.98, T.99, S.100, T.164, S.167, S.168, G.412, G.413, E.417, I.449, L.453, F.483, E.498 Ligands: BEF.17, MG.18 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.45, F:N.64, F:G.97, F:G.97, F:T.99, F:T.99, F:S.100, F:S.167, F:S.168, F:G.413, F:E.417, F:E.498 ADP.19: 21 residues within 4Å: Chain G: M.46, G.47, N.66, D.98, G.99, T.100, N.101, L.102, P.165, S.169, G.422, A.423, G.424, E.427, V.459, L.463, I.501, D.519, K.524 Ligands: BEF.20, MG.21 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:G.47, G:N.66, G:D.98, G:G.99, G:G.99, G:T.100, G:T.100, G:N.101, G:L.102, G:P.165, G:S.169, G:A.423, G:G.424, G:E.427, G:D.519, G:K.524 ADP.22: 22 residues within 4Å: Chain H: N.36, L.37, G.38, P.39, K.57, D.89, G.90, T.91, T.92, T.93, T.160, G.414, A.415, G.416, I.454, L.458, V.491, L.493, I.506, D.508 Ligands: BEF.23, MG.24 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:G.38, H:G.90, H:G.90, H:T.91, H:T.92, H:T.92, H:T.93, H:T.160, H:T.160, H:A.415, H:G.416, H:D.508 Salt bridges: H:K.57, H:K.161, H:K.161 ADP.25: 23 residues within 4Å: Chain I: S.43, L.44, G.45, P.46, D.96, G.97, T.98, T.99, S.100, T.162, S.165, S.166, G.421, G.422, I.458, L.462, L.502, E.512, V.517, E.519, K.524 Ligands: BEF.26, MG.27 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:S.43, I:G.45, I:G.97, I:G.97, I:T.99, I:S.100, I:S.165, I:S.165, I:S.165, I:S.166, I:G.422, I:E.519, I:K.524 ADP.28: 22 residues within 4Å: Chain J: T.36, L.37, G.38, P.39, N.58, D.90, G.91, T.92, T.93, S.94, T.159, S.162, S.163, G.403, G.404, L.444, L.472, I.487, E.489, K.494 Ligands: BEF.29, MG.30 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.38, J:N.58, J:G.91, J:G.91, J:T.93, J:S.94, J:S.162, J:S.163, J:G.404, J:G.405, J:E.489, J:K.494 Salt bridges: J:K.164, J:K.164 ADP.31: 25 residues within 4Å: Chain K: S.38, L.39, G.40, P.41, N.59, D.91, G.92, T.93, T.94, S.95, T.156, S.159, S.160, K.161, G.414, G.415, L.454, I.482, S.483, V.484, R.485, I.497, Q.499 Ligands: BEF.32, MG.33 19 PLIP interactions: 19 interactions with chain K Hydrogen bonds: K:G.40, K:N.59, K:G.92, K:G.92, K:T.94, K:T.94, K:S.95, K:S.95, K:S.95, K:S.159, K:S.159, K:S.160, K:G.414, K:G.415, K:V.484, K:R.485, K:Q.499 Salt bridges: K:K.161, K:K.161 ADP.34: 20 residues within 4Å: Chain L: S.64, L.65, G.66, P.67, N.85, D.117, G.118, T.119, T.120, G.121, T.186, S.190, G.443, G.444, L.483, C.514, V.527, D.529 Ligands: BEF.35, MG.36 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:S.64, L:G.66, L:N.85, L:G.118, L:T.120, L:T.120, L:G.121, L:S.190, L:G.443, L:G.444, L:D.529 ADP.37: 21 residues within 4Å: Chain M: C.38, L.39, G.40, D.91, G.92, T.93, T.94, T.95, T.161, G.471, G.472, G.473, E.476, L.512, I.540, G.542, Y.553, I.555, E.557 Ligands: BEF.38, MG.39 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:C.38, M:G.40, M:G.92, M:G.92, M:T.93, M:T.94, M:T.94, M:T.95, M:T.161, M:G.472, M:G.473, M:E.476, M:G.542, M:E.557 ADP.40: 21 residues within 4Å: Chain N: T.43, L.44, G.45, N.64, D.96, G.97, T.98, T.99, S.100, T.164, S.167, S.168, G.412, G.413, E.417, I.449, L.453, F.483, E.498 Ligands: BEF.41, MG.42 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.45, N:N.64, N:G.97, N:G.97, N:T.99, N:T.99, N:S.100, N:S.167, N:S.168, N:G.413, N:E.417, N:E.498 ADP.43: 21 residues within 4Å: Chain O: M.46, G.47, N.66, D.98, G.99, T.100, N.101, L.102, P.165, S.169, G.422, A.423, G.424, E.427, V.459, L.463, I.501, D.519, K.524 Ligands: BEF.44, MG.45 15 PLIP interactions: 15 interactions with chain O Hydrogen bonds: O:G.47, O:N.66, O:G.99, O:G.99, O:T.100, O:T.100, O:N.101, O:L.102, O:P.165, O:S.169, O:A.423, O:G.424, O:E.427, O:D.519, O:K.524 ADP.46: 22 residues within 4Å: Chain P: N.36, L.37, G.38, P.39, K.57, D.89, G.90, T.91, T.92, T.93, T.160, G.414, A.415, G.416, I.454, L.458, V.491, L.493, I.506, D.508 Ligands: BEF.47, MG.48 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:G.38, P:G.90, P:G.90, P:T.91, P:T.92, P:T.92, P:T.93, P:T.160, P:T.160, P:A.415, P:G.416, P:D.508 Salt bridges: P:K.57, P:K.161, P:K.161

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

BEF.2: 11 residues within 4Å: Chain A: N.64, D.65, G.66, D.96, G.97, T.98, T.99, K.167, D.404 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 11 residues within 4Å: Chain B: T.36, N.58, D.59, G.60, D.90, T.92, T.93, K.164, D.386 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.8: 11 residues within 4Å: Chain C: N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.396 Ligands: ADP.7, MG.9 No protein-ligand interaction detected (PLIP) BEF.11: 10 residues within 4Å: Chain D: N.85, D.86, G.87, D.117, T.119, T.120, K.191, D.425 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP) BEF.14: 8 residues within 4Å: Chain E: D.60, D.91, T.93, K.162, R.450, D.454 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP) BEF.17: 11 residues within 4Å: Chain F: N.64, D.65, G.66, D.96, G.97, T.98, T.99, K.169, D.395 Ligands: ADP.16, MG.18 No protein-ligand interaction detected (PLIP) BEF.20: 9 residues within 4Å: Chain G: D.67, G.97, D.98, G.99, T.100, K.170, D.403 Ligands: ADP.19, MG.21 No protein-ligand interaction detected (PLIP) BEF.23: 12 residues within 4Å: Chain H: K.57, D.58, G.59, D.89, G.90, T.91, T.92, T.160, K.161, D.397 Ligands: ADP.22, MG.24 No protein-ligand interaction detected (PLIP) BEF.26: 11 residues within 4Å: Chain I: N.64, D.65, G.66, D.96, G.97, T.98, T.99, K.167, D.404 Ligands: ADP.25, MG.27 No protein-ligand interaction detected (PLIP) BEF.29: 11 residues within 4Å: Chain J: T.36, N.58, D.59, G.60, D.90, T.92, T.93, K.164, D.386 Ligands: ADP.28, MG.30 No protein-ligand interaction detected (PLIP) BEF.32: 11 residues within 4Å: Chain K: N.59, D.60, G.61, D.91, G.92, T.93, T.94, K.161, D.396 Ligands: ADP.31, MG.33 No protein-ligand interaction detected (PLIP) BEF.35: 10 residues within 4Å: Chain L: N.85, D.86, G.87, D.117, T.119, T.120, K.191, D.425 Ligands: ADP.34, MG.36 No protein-ligand interaction detected (PLIP) BEF.38: 8 residues within 4Å: Chain M: D.60, D.91, T.93, K.162, R.450, D.454 Ligands: ADP.37, MG.39 No protein-ligand interaction detected (PLIP) BEF.41: 11 residues within 4Å: Chain N: N.64, D.65, G.66, D.96, G.97, T.98, T.99, K.169, D.395 Ligands: ADP.40, MG.42 No protein-ligand interaction detected (PLIP) BEF.44: 9 residues within 4Å: Chain O: D.67, G.97, D.98, G.99, T.100, K.170, D.403 Ligands: ADP.43, MG.45 No protein-ligand interaction detected (PLIP) BEF.47: 12 residues within 4Å: Chain P: K.57, D.58, G.59, D.89, G.90, T.91, T.92, T.160, K.161, D.397 Ligands: ADP.46, MG.48 No protein-ligand interaction detected (PLIP)

16 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.96, K.167 Ligands: ADP.1, BEF.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.96, A:D.96 MG.6: 5 residues within 4Å: Chain B: D.90, T.160, K.164 Ligands: ADP.4, BEF.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.90, B:D.90 MG.9: 5 residues within 4Å: Chain C: D.91, S.157, K.161 Ligands: ADP.7, BEF.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.91 MG.12: 4 residues within 4Å: Chain D: D.117, S.187 Ligands: ADP.10, BEF.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.117, D:D.117 MG.15: 3 residues within 4Å: Chain E: D.91 Ligands: ADP.13, BEF.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.91, E:D.91 MG.18: 5 residues within 4Å: Chain F: D.96, A.165, K.169 Ligands: ADP.16, BEF.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.96, F:D.96 MG.21: 4 residues within 4Å: Chain G: D.98, V.166 Ligands: ADP.19, BEF.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.98 MG.24: 5 residues within 4Å: Chain H: D.89, T.160, K.161 Ligands: ADP.22, BEF.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.89, H:D.89 MG.27: 4 residues within 4Å: Chain I: D.96, K.167 Ligands: ADP.25, BEF.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.96, I:D.96 MG.30: 5 residues within 4Å: Chain J: D.90, T.160, K.164 Ligands: ADP.28, BEF.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.90, J:D.90 MG.33: 5 residues within 4Å: Chain K: D.91, S.157, K.161 Ligands: ADP.31, BEF.32 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.91 MG.36: 4 residues within 4Å: Chain L: D.117, S.187 Ligands: ADP.34, BEF.35 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.117, L:D.117 MG.39: 3 residues within 4Å: Chain M: D.91 Ligands: ADP.37, BEF.38 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.91, M:D.91 MG.42: 5 residues within 4Å: Chain N: D.96, A.165, K.169 Ligands: ADP.40, BEF.41 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.96, N:D.96 MG.45: 4 residues within 4Å: Chain O: D.98, V.166 Ligands: ADP.43, BEF.44 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.98 MG.48: 5 residues within 4Å: Chain P: D.89, T.160, K.161 Ligands: ADP.46, BEF.47 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.89, P:D.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalisman, N. et al., The Crystal Structures of the Eukaryotic Chaperonin Cct Reveal its Functional Partitioning. Structure (2013)

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 DELTA: CK
T-COMPLEX PROTEIN 1 SUBUNIT EPSILON: DL
T-COMPLEX PROTEIN 1 SUBUNIT GAMMA: EM
T-COMPLEX PROTEIN 1 SUBUNIT ETA: FN
T-COMPLEX PROTEIN 1 SUBUNIT THETA: GO
T-COMPLEX PROTEIN 1 SUBUNIT ZETA: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

I
Ba

B
BB

J
Bb

C
BD

K
Bd

D
BE

L
Be

E
BG

M
Bg

F
BH

N
Bh

G
BQ

O
Bq

H
BZ

P
Bz

T-COMPLEX PROTEIN 1 SUBUNIT ALPHA

T-COMPLEX PROTEIN 1 SUBUNIT BETA

T-COMPLEX PROTEIN 1 SUBUNIT DELTA

T-COMPLEX PROTEIN 1 SUBUNIT EPSILON

T-COMPLEX PROTEIN 1 SUBUNIT GAMMA

T-COMPLEX PROTEIN 1 SUBUNIT ETA

T-COMPLEX PROTEIN 1 SUBUNIT THETA

T-COMPLEX PROTEIN 1 SUBUNIT ZETA

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