SMTL ID : 8shp.1

CCT G beta 5 complex closed state 13

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 22 residues within 4Å: Chain B: 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, L.489, R.495, V.502, E.504 Ligands: MG.2, AF3.3 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.36, B:G.88, B:T.89, B:T.90, B:T.90, B:S.91, B:S.156, B:S.157, B:G.411, B:R.495, B:E.504 Water bridges: B:T.90 Salt bridges: B:K.158, B:K.158 ADP.4: 23 residues within 4Å: Chain C: T.41, 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, K.499 Ligands: MG.5, AF3.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.43, C:G.97, C:T.98, C:T.99, C:S.100, C:S.100, C:S.100, C:S.100, C:S.167, C:S.168, C:S.168, C:G.409, C:E.494, C:K.499 Water bridges: C:T.99 Salt bridges: C:K.169 ADP.7: 21 residues within 4Å: Chain D: 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 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.35, D:G.87, D:T.89, D:T.89, D:S.90, D:N.154, D:S.155, D:G.407, D:Q.492 Salt bridges: D:K.156, D:K.156 ADP.10: 20 residues within 4Å: Chain E: 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 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.52, E:G.104, E:G.104, E:T.106, E:S.174, E:G.421, E:E.507 Salt bridges: E:K.175, E:K.175 ADP.13: 21 residues within 4Å: Chain F: C.38, L.39, G.40, P.41, G.92, T.93, T.94, S.95, T.159, T.160, G.408, G.409, L.449, V.478, N.479, G.480, E.481, I.493, E.495 Ligands: MG.14, AF3.15 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.40, F:G.92, F:T.93, F:T.94, F:S.95, F:S.95, F:T.160, F:G.409, F:G.480, F:E.481, F:E.495 Salt bridges: F:K.161 ADP.16: 22 residues within 4Å: Chain G: T.39, L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, T.161, S.164, S.165, G.408, G.409, G.410, V.477, I.479, V.492, E.494, R.499 Ligands: MG.17, AF3.18 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.41, G:G.93, G:T.94, G:T.94, G:T.95, G:S.96, G:S.96, G:S.164, G:S.164, G:S.165, G:G.409, G:G.410, G:E.494, G:R.499 Salt bridges: G:K.166 ADP.19: 21 residues within 4Å: Chain H: 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, G.412, L.479, I.481, I.496, D.498 Ligands: MG.20, AF3.21 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Y.46, H:Y.46, H:G.47, H:D.98, H:G.99, H:N.101, H:F.102, H:S.169, H:G.411, H:G.412, H:D.498 Salt bridges: H:K.170, H:K.170 ADP.22: 21 residues within 4Å: Chain I: 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 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:G.39, I:D.90, I:G.91, I:T.93, I:S.94, I:A.411, I:G.412, I:D.496 Salt bridges: I:K.58, I:K.159, I:K.159 ADP.25: 23 residues within 4Å: Chain J: 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, L.489, R.495, V.502, E.504 Ligands: MG.26, AF3.27 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:S.34, J:G.36, J:G.88, J:T.89, J:T.90, J:T.90, J:T.90, J:T.90, J:S.91, J:S.156, J:S.156, J:S.157, J:G.411, J:R.495, J:E.504 Salt bridges: J:K.158, J:K.158 ADP.28: 21 residues within 4Å: Chain K: T.41, L.42, G.43, P.44, D.96, G.97, T.98, T.99, S.100, T.164, S.167, S.168, K.169, G.408, G.409, L.477, M.479, I.492, E.494 Ligands: MG.29, AF3.30 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:G.43, K:G.97, K:T.98, K:T.99, K:T.99, K:S.100, K:S.100, K:S.100, K:S.100, K:S.167, K:S.167, K:S.168, K:S.168, K:G.409, K:E.494 Salt bridges: K:K.169 ADP.31: 21 residues within 4Å: Chain L: S.33, 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.490, Q.492 Ligands: MG.32, AF3.33 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:S.33, L:G.35, L:D.86, L:G.87, L:T.88, L:T.89, L:T.89, L:S.90, L:N.154, L:S.155, L:G.407, L:Q.492 Salt bridges: L:K.156, L:K.156 ADP.34: 24 residues within 4Å: Chain M: S.50, L.51, G.52, P.53, D.103, G.104, T.105, T.106, G.107, 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 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:G.52, M:G.104, M:T.105, M:T.105, M:T.106, M:G.107, M:S.174, M:G.421, M:E.507, M:K.512 Salt bridges: M:K.175, M:K.175 ADP.37: 22 residues within 4Å: Chain N: 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, I.493, E.495, K.500 Ligands: MG.38, AF3.39 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.40, N:G.92, N:G.92, N:T.94, N:T.94, N:S.95, N:G.409, N:G.480, N:K.500, N:K.500 Salt bridges: N:K.161, N:K.161 ADP.40: 22 residues within 4Å: Chain O: 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, V.492, E.494, R.499 Ligands: MG.41, AF3.42 16 PLIP interactions: 16 interactions with chain O Hydrogen bonds: O:G.41, O:G.93, O:T.94, O:T.95, O:T.95, O:T.95, O:S.96, O:S.164, O:S.164, O:S.165, O:S.165, O:G.409, O:E.494, O:R.499 Salt bridges: O:K.166, O:K.166 ADP.43: 19 residues within 4Å: Chain P: 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, I.481, M.491, I.496, D.498 Ligands: MG.44, AF3.45 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:Y.46, P:G.47, P:D.98, P:G.99, P:T.100, P:N.101, P:F.102, P:S.169, P:G.411, P:G.412, P:D.498 Salt bridges: P:K.170, P:K.170 ADP.46: 21 residues within 4Å: Chain Q: 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, L.451, V.479, L.481, V.494, D.496 Ligands: MG.47, AF3.48 11 PLIP interactions: 11 interactions with chain Q Hydrogen bonds: Q:G.39, Q:G.91, Q:T.92, Q:T.93, Q:T.93, Q:S.94, Q:A.411, Q:G.412, Q:D.496 Salt bridges: Q:K.159, Q:K.159

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: D.87, K.158 Ligands: ADP.1, AF3.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.87 MG.5: 4 residues within 4Å: Chain C: D.96, T.165 Ligands: ADP.4, AF3.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.96, C:D.96 MG.8: 4 residues within 4Å: Chain D: D.86, K.156 Ligands: ADP.7, AF3.9 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.86, D:D.86 MG.11: 3 residues within 4Å: Chain E: D.103 Ligands: ADP.10, AF3.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.103 MG.14: 4 residues within 4Å: Chain F: D.91, G.92 Ligands: ADP.13, AF3.15 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain G: D.92, A.162 Ligands: ADP.16, AF3.18 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.92, G:D.92 MG.20: 5 residues within 4Å: Chain H: D.98, G.99, K.170 Ligands: ADP.19, AF3.21 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.98, H:D.98 MG.23: 4 residues within 4Å: Chain I: D.90, K.159 Ligands: ADP.22, AF3.24 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.90, I:D.90 MG.26: 4 residues within 4Å: Chain J: D.87, G.88 Ligands: ADP.25, AF3.27 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.87 MG.29: 3 residues within 4Å: Chain K: D.96 Ligands: ADP.28, AF3.30 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.96, K:D.96 MG.32: 3 residues within 4Å: Chain L: D.86 Ligands: ADP.31, AF3.33 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.86 MG.35: 4 residues within 4Å: Chain M: D.103, K.175 Ligands: ADP.34, AF3.36 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.103 MG.38: 4 residues within 4Å: Chain N: D.91, K.161 Ligands: ADP.37, AF3.39 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.91 MG.41: 4 residues within 4Å: Chain O: D.92, A.162 Ligands: ADP.40, AF3.42 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.92, O:D.92 MG.44: 4 residues within 4Å: Chain P: D.98, K.170 Ligands: ADP.43, AF3.45 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.98, P:D.98 MG.47: 4 residues within 4Å: Chain Q: D.90, K.159 Ligands: ADP.46, AF3.48 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.90

16 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 11 residues within 4Å: Chain B: N.55, D.56, G.57, G.86, D.87, T.89, T.90, K.158, D.393 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP) AF3.6: 8 residues within 4Å: Chain C: D.65, D.96, T.98, T.99, K.169, D.391 Ligands: ADP.4, MG.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.96 AF3.9: 11 residues within 4Å: Chain D: 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: 11 residues within 4Å: Chain E: N.71, D.72, G.73, D.103, G.104, 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 F: D.60, G.61, G.90, D.91, T.93, T.94, K.161, D.391 Ligands: ADP.13, MG.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.60 AF3.18: 10 residues within 4Å: Chain G: 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 H: 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 H Metal complexes: H:T.100 AF3.24: 10 residues within 4Å: Chain I: D.59, G.60, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.22, MG.23 No protein-ligand interaction detected (PLIP) AF3.27: 10 residues within 4Å: Chain J: D.56, G.57, G.86, D.87, T.89, T.90, K.158, D.393 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP) AF3.30: 10 residues within 4Å: Chain K: N.64, D.65, G.66, D.96, T.98, T.99, K.169, D.391 Ligands: ADP.28, MG.29 No protein-ligand interaction detected (PLIP) AF3.33: 10 residues within 4Å: Chain L: D.55, G.56, 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: 10 residues within 4Å: Chain M: N.71, D.72, G.73, D.103, 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 N: D.60, G.61, G.90, D.91, T.93, T.94, K.161, D.391 Ligands: ADP.37, MG.38 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.60 AF3.42: 9 residues within 4Å: Chain O: 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: 11 residues within 4Å: Chain P: D.67, A.68, G.97, D.98, G.99, T.100, N.101, K.170, D.393 Ligands: ADP.43, MG.44 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.100 AF3.48: 10 residues within 4Å: Chain Q: D.59, G.60, G.89, D.90, 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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
A

J
a

C
B

K
b

D
D

L
d

E
E

M
e

F
G

N
g

G
H

O
h

H
Q

P
q

I
Z

Q
z

R
P

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

Phosducin-like protein

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