SMTL ID : 8shq.1

CCT G beta 5 complex closed state 12

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-2-2-2-2-2-2-mer

Ligands

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

ADP.1: 22 residues within 4Å: Chain C: S.34, L.35, G.36, P.37, D.87, G.88, T.89, T.90, S.91, T.153, S.156, S.157, K.158, G.410, G.411, L.451, L.487, R.495, V.502, E.504 Ligands: MG.2, AF3.3 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.36, C:G.88, C:T.89, C:T.90, C:T.90, C:S.91, C:S.156, C:S.156, C:S.157, C:S.157, C:G.411, C:R.495, C:E.504 Water bridges: C:T.90, C:T.90 Salt bridges: C:K.158, C:K.158 ADP.4: 23 residues within 4Å: Chain D: L.42, G.43, P.44, D.96, G.97, T.98, T.99, S.100, T.164, T.165, S.167, S.168, G.408, G.409, G.410, I.449, L.477, M.479, I.492, E.494, K.499 Ligands: MG.5, AF3.6 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.43, D:G.97, D:T.98, D:T.99, D:S.100, D:S.100, D:S.100, D:S.100, D:S.167, D:S.168, D:G.409, D:G.410, D:E.494, D:K.499 Water bridges: D:T.99 Salt bridges: D:K.169 ADP.7: 21 residues within 4Å: Chain E: L.34, G.35, P.36, D.86, G.87, T.88, T.89, S.90, T.151, S.152, N.154, S.155, K.156, G.406, G.407, L.447, I.475, V.490, Q.492 Ligands: MG.8, AF3.9 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.35, E:G.87, E:T.88, E:T.89, E:T.89, E:S.90, E:S.90, E:N.154, E:S.155, E:G.407, E:G.408, E:Q.492 Salt bridges: E:K.156, E:K.156 ADP.10: 20 residues within 4Å: Chain F: L.51, G.52, P.53, D.103, G.104, T.105, T.106, T.171, S.174, K.175, G.420, G.421, L.461, I.490, C.492, L.493, V.505, E.507 Ligands: MG.11, AF3.12 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.52, F:G.104, F:T.106, F:T.106, F:S.174, F:S.174, F:G.421, F:E.507 Salt bridges: F:K.175, F:K.175 ADP.13: 21 residues within 4Å: Chain G: C.38, L.39, G.40, P.41, G.92, T.93, T.94, S.95, T.159, T.160, K.161, G.408, G.409, G.410, L.449, V.478, G.480, I.493, E.495 Ligands: MG.14, AF3.15 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.40, G:G.92, G:T.93, G:T.94, G:S.95, G:T.160, G:G.409, G:G.410, G:G.480, G:E.495 Salt bridges: G:K.161 ADP.16: 23 residues within 4Å: Chain H: T.39, L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, T.161, A.162, S.164, S.165, G.408, G.409, L.449, V.477, I.479, V.492, E.494, R.499 Ligands: MG.17, AF3.18 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.41, H:G.93, H:T.95, H:S.96, H:S.164, H:S.164, H:S.165, H:G.409, H:G.410, H:E.494, H:R.499 Salt bridges: H:K.166 ADP.19: 22 residues within 4Å: Chain I: A.45, Y.46, G.47, P.48, D.98, G.99, T.100, N.101, F.102, M.168, S.169, K.170, G.410, G.411, L.451, L.479, I.481, M.491, I.496, D.498 Ligands: MG.20, AF3.21 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:Y.46, I:Y.46, I:G.47, I:D.98, I:D.98, I:G.99, I:T.100, I:N.101, I:F.102, I:S.169, I:G.411, I:G.412, I:D.498 Salt bridges: I:K.170, I:K.170 ADP.22: 21 residues within 4Å: Chain J: N.37, L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.158, K.159, G.410, A.411, G.412, L.451, V.479, L.481, V.494, D.496 Ligands: MG.23, AF3.24 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:G.39, J:K.58, J:D.90, J:G.91, J:T.93, J:S.94, J:T.158, J:A.411, J:G.412, J:D.496 Salt bridges: J:K.159, J:K.159 ADP.25: 22 residues within 4Å: Chain K: S.34, L.35, G.36, P.37, D.87, G.88, T.89, T.90, S.91, T.153, S.156, S.157, K.158, G.410, G.411, L.451, L.487, R.495, V.502, E.504 Ligands: MG.26, AF3.27 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:S.34, K:G.36, K:G.88, K:T.89, K:T.90, K:T.90, K:T.90, K:S.91, K:S.156, K:S.157, K:G.411, K:R.495, K:E.504 Salt bridges: K:K.158, K:K.158 ADP.28: 21 residues within 4Å: Chain L: L.42, G.43, P.44, D.96, G.97, T.98, T.99, S.100, T.164, T.165, S.167, S.168, G.408, G.409, I.449, L.477, M.479, I.492, E.494 Ligands: MG.29, AF3.30 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:T.41, L:G.43, L:G.97, L:T.98, L:T.99, L:T.99, L:S.100, L:S.100, L:S.100, L:S.100, L:S.167, L:S.167, L:S.168, L:G.409, L:E.494 ADP.31: 21 residues within 4Å: Chain M: L.34, G.35, P.36, D.86, G.87, T.88, T.89, S.90, T.151, N.154, S.155, K.156, G.406, G.407, L.447, I.475, V.477, V.490, Q.492 Ligands: MG.32, AF3.33 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:S.33, M:G.35, M:D.86, M:G.87, M:T.88, M:T.89, M:T.89, M:S.90, M:N.154, M:S.155, M:G.407 Salt bridges: M:K.156 ADP.34: 23 residues within 4Å: Chain N: S.50, L.51, G.52, P.53, D.103, G.104, T.105, T.106, T.170, T.171, S.174, K.175, G.420, G.421, L.461, I.490, C.492, L.493, M.500, V.505, E.507 Ligands: MG.35, AF3.36 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:G.52, N:G.104, N:T.105, N:T.106, N:T.106, N:S.174, N:S.174, N:G.421, N:E.507 Salt bridges: N:K.175, N:K.175 ADP.37: 22 residues within 4Å: Chain O: C.38, L.39, G.40, P.41, D.91, G.92, T.93, T.94, S.95, T.159, T.160, K.161, G.408, G.409, L.449, V.478, G.480, L.491, I.493, E.495 Ligands: MG.38, AF3.39 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:G.40, O:G.92, O:G.92, O:T.94, O:T.94, O:S.95, O:G.409, O:G.410, O:G.480, O:E.495 Salt bridges: O:K.161, O:K.161 ADP.40: 23 residues within 4Å: Chain P: T.39, L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, T.161, A.162, S.164, S.165, G.408, G.409, L.449, V.477, I.479, V.492, E.494, R.499 Ligands: MG.41, AF3.42 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:G.41, P:G.93, P:T.94, P:T.95, P:T.95, P:T.95, P:S.164, P:S.164, P:S.165, P:S.165, P:G.409, P:E.494, P:R.499 Salt bridges: P:K.166, P:K.166 ADP.43: 19 residues within 4Å: Chain Q: Y.46, G.47, P.48, D.98, G.99, T.100, N.101, F.102, M.168, S.169, K.170, G.410, G.411, L.451, I.481, I.496, D.498 Ligands: MG.44, AF3.45 13 PLIP interactions: 13 interactions with chain Q Hydrogen bonds: Q:Y.46, Q:G.47, Q:D.98, Q:G.99, Q:G.99, Q:N.101, Q:F.102, Q:S.169, Q:G.411, Q:G.412, Q:D.498 Salt bridges: Q:K.170, Q:K.170 ADP.46: 22 residues within 4Å: Chain R: N.37, L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.154, T.158, K.159, G.410, A.411, G.412, L.451, V.479, L.481, V.494, D.496 Ligands: MG.47, AF3.48 12 PLIP interactions: 12 interactions with chain R Hydrogen bonds: R:G.39, R:G.91, R:G.91, R:T.93, R:S.94, R:A.411, R:G.412, R:D.496, R:K.501, R:K.501 Salt bridges: R:K.159, R:K.159

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: D.87 Ligands: ADP.1, AF3.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.87 MG.5: 4 residues within 4Å: Chain D: D.96, T.165 Ligands: ADP.4, AF3.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.96, D:D.96 MG.8: 3 residues within 4Å: Chain E: D.86 Ligands: ADP.7, AF3.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.86, E:D.86 MG.11: 3 residues within 4Å: Chain F: D.103 Ligands: ADP.10, AF3.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.103 MG.14: 3 residues within 4Å: Chain G: D.91 Ligands: ADP.13, AF3.15 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain H: D.92 Ligands: ADP.16, AF3.18 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.92, H:D.92 MG.20: 4 residues within 4Å: Chain I: D.98, K.170 Ligands: ADP.19, AF3.21 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.98, I:D.98 MG.23: 2 residues within 4Å: Chain J: D.90 Ligands: ADP.22 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.90, J:D.90 MG.26: 3 residues within 4Å: Chain K: D.87 Ligands: ADP.25, AF3.27 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.87 MG.29: 4 residues within 4Å: Chain L: D.96, T.165 Ligands: ADP.28, AF3.30 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.96 MG.32: 5 residues within 4Å: Chain M: D.86, S.155, K.156 Ligands: ADP.31, AF3.33 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain N: D.103 Ligands: ADP.34, AF3.36 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.103 MG.38: 4 residues within 4Å: Chain O: D.91, K.161 Ligands: ADP.37, AF3.39 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.91 MG.41: 4 residues within 4Å: Chain P: D.92, A.162 Ligands: ADP.40, AF3.42 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.92, P:D.92 MG.44: 3 residues within 4Å: Chain Q: D.98, K.170 Ligands: ADP.43 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.98, Q:D.98 MG.47: 3 residues within 4Å: Chain R: D.90 Ligands: ADP.46, AF3.48 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:D.90

16 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 10 residues within 4Å: Chain C: N.55, D.56, G.57, D.87, T.89, T.90, K.158, D.393 Ligands: ADP.1, MG.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.56 AF3.6: 10 residues within 4Å: Chain D: D.65, G.66, G.95, D.96, T.98, T.99, K.169, D.391 Ligands: ADP.4, MG.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.96 AF3.9: 11 residues within 4Å: Chain E: N.54, D.55, G.56, G.85, D.86, T.88, T.89, K.156, D.389 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) AF3.12: 10 residues within 4Å: Chain F: N.71, D.72, G.73, D.103, T.105, T.106, K.175, D.403 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) AF3.15: 10 residues within 4Å: Chain G: D.60, G.61, G.90, D.91, T.93, T.94, K.161, D.391 Ligands: ADP.13, MG.14 No protein-ligand interaction detected (PLIP) AF3.18: 10 residues within 4Å: Chain H: N.60, D.61, G.62, D.92, T.94, T.95, K.166, D.391 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP) AF3.21: 11 residues within 4Å: Chain I: D.67, A.68, G.97, D.98, G.99, T.100, N.101, K.170, D.393 Ligands: ADP.19, MG.20 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.100 AF3.24: 9 residues within 4Å: Chain J: D.59, G.60, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.22 No protein-ligand interaction detected (PLIP) AF3.27: 10 residues within 4Å: Chain K: D.56, G.57, G.86, D.87, T.89, T.90, K.158, D.393 Ligands: ADP.25, MG.26 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.56 AF3.30: 9 residues within 4Å: Chain L: N.64, D.65, G.66, D.96, G.97, T.98, T.99 Ligands: ADP.28, MG.29 No protein-ligand interaction detected (PLIP) AF3.33: 12 residues within 4Å: Chain M: N.54, D.55, G.56, G.85, D.86, G.87, T.88, T.89, K.156, D.389 Ligands: ADP.31, MG.32 No protein-ligand interaction detected (PLIP) AF3.36: 11 residues within 4Å: Chain N: N.71, D.72, G.73, D.103, G.104, T.105, T.106, K.175, D.403 Ligands: ADP.34, MG.35 No protein-ligand interaction detected (PLIP) AF3.39: 10 residues within 4Å: Chain O: D.60, G.61, G.90, D.91, T.93, T.94, K.161, D.391 Ligands: ADP.37, MG.38 No protein-ligand interaction detected (PLIP) AF3.42: 11 residues within 4Å: Chain P: T.39, N.60, D.61, G.62, D.92, T.94, T.95, K.166, D.391 Ligands: ADP.40, MG.41 No protein-ligand interaction detected (PLIP) AF3.45: 9 residues within 4Å: Chain Q: D.67, A.68, D.98, G.99, T.100, N.101, K.170, D.393 Ligands: ADP.43 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.100 AF3.48: 11 residues within 4Å: Chain R: D.59, G.60, G.89, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.46, MG.47 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Visualizing the chaperone-mediated folding trajectory of the G protein beta 5 beta-propeller. Mol.Cell (2023)

Release Date

2023-10-25

Peptides

Phosducin-like protein: A
Guanine nucleotide-binding protein subunit beta-5: B
T-complex protein 1 subunit alpha: CK
T-complex protein 1 subunit beta: DL
T-complex protein 1 subunit delta: EM
T-complex protein 1 subunit epsilon: FN
T-complex protein 1 subunit gamma: GO
T-complex protein 1 subunit eta, N-terminally processed: HP
T-complex protein 1 subunit theta: IQ
T-complex protein 1 subunit zeta: JR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
N

C
A

K
a

D
B

L
b

E
D

M
d

F
E

N
e

G
G

O
g

H
H

P
h

I
Q

Q
q

J
Z

R
z

Phosducin-like protein

Guanine nucleotide-binding protein subunit beta-5

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, N-terminally processed

T-complex protein 1 subunit theta

T-complex protein 1 subunit zeta

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