SMTL ID : 8i1u.1

Human TRiC-PhLP2A complex in the closed state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: S.35, L.36, G.37, P.38, D.88, G.89, T.90, T.91, S.92, T.154, S.157, S.158, K.159, G.411, G.412, L.452, L.488, R.496, V.503, E.505 Ligands: MG.2, AF3.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.35, A:G.37, A:G.89, A:T.90, A:T.91, A:S.92, A:S.157, A:S.158, A:G.412, A:G.413, A:R.496, A:R.496, A:E.505 Salt bridges: A:K.159, A:K.159 ADP.4: 22 residues within 4Å: Chain B: T.42, L.43, G.44, P.45, D.97, G.98, T.99, T.100, T.165, S.168, S.169, K.170, G.409, G.410, E.414, I.450, L.478, I.493, E.495, K.500 Ligands: MG.5, AF3.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.44, B:G.98, B:T.99, B:S.168, B:S.168, B:S.169, B:S.169, B:G.410, B:E.495, B:K.500 Salt bridges: B:K.170 ADP.7: 25 residues within 4Å: Chain C: C.40, L.41, G.42, P.43, D.93, G.94, T.95, T.96, S.97, T.161, T.162, K.163, G.410, G.411, G.412, L.451, V.480, N.481, G.482, E.483, I.495, E.497, K.502 Ligands: MG.8, AF3.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.42, C:G.94, C:G.94, C:T.95, C:T.96, C:S.97, C:T.162, C:G.411, C:G.412, C:G.482, C:K.502, C:K.502 Salt bridges: C:K.163, C:K.163 ADP.10: 18 residues within 4Å: Chain D: L.52, G.53, P.54, D.104, G.105, T.106, T.107, T.169, S.170, N.172, S.173, G.424, G.425, L.465, I.493, V.508 Ligands: MG.11, AF3.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.53, D:G.105, D:T.106, D:T.107, D:T.107, D:S.108, D:N.172, D:S.173, D:S.173, D:G.425 Salt bridges: D:K.174 ADP.13: 19 residues within 4Å: Chain E: L.52, G.53, P.54, D.104, G.105, T.106, T.107, G.174, S.175, K.176, G.421, G.422, L.462, I.491, L.494, V.506, E.508 Ligands: MG.14, AF3.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.53, E:D.104, E:G.105, E:T.106, E:T.107, E:T.107, E:S.175, E:S.175, E:G.422, E:G.423, E:E.508, E:E.508 Salt bridges: E:K.176, E:K.176 ADP.16: 18 residues within 4Å: Chain F: L.38, G.39, P.40, D.90, G.91, T.92, T.93, S.94, T.158, G.410, A.411, L.451, V.479, L.481, V.494, D.496 Ligands: MG.17, AF3.18 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.39, F:G.91, F:T.92, F:T.92, F:T.93, F:T.93, F:S.94, F:A.411 Salt bridges: F:K.159 ADP.19: 17 residues within 4Å: Chain G: T.39, L.40, G.41, P.42, D.92, G.93, T.94, T.95, S.96, S.164, S.165, G.408, G.409, L.449, R.499 Ligands: MG.20, AF3.21 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:T.39, G:G.41, G:G.93, G:T.94, G:T.95, G:T.95, G:S.96, G:S.164, G:S.164, G:S.165, G:G.409, G:R.499 ADP.22: 19 residues within 4Å: Chain H: Y.47, G.48, P.49, D.99, G.100, T.101, N.102, F.103, M.169, S.170, G.411, G.412, L.452, L.480, I.482, I.497, D.499 Ligands: MG.23, AF3.24 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:Y.47, H:G.48, H:G.100, H:T.101, H:T.101, H:N.102, H:F.103, H:S.170, H:G.412, H:D.499 Salt bridges: H:K.171, H:K.171 ADP.25: 15 residues within 4Å: Chain I: G.37, P.38, D.88, G.89, T.90, T.91, S.92, T.154, S.157, S.158, G.411, G.412, K.510 Ligands: MG.26, AF3.27 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:G.37, I:G.89, I:T.90, I:T.91, I:S.92, I:T.154, I:S.157, I:S.158, I:S.158, I:G.412, I:K.510 Salt bridges: I:K.159, I:K.159 ADP.28: 21 residues within 4Å: Chain J: L.43, G.44, P.45, D.97, G.98, T.99, T.100, S.101, T.165, S.168, S.169, K.170, G.409, G.410, I.450, M.480, I.493, E.495, K.500 Ligands: MG.29, AF3.30 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.44, J:G.98, J:T.100, J:S.101, J:T.165, J:S.168, J:S.168, J:S.169, J:G.410, J:E.495, J:K.500, J:K.500 Salt bridges: J:K.170, J:K.170 ADP.31: 20 residues within 4Å: Chain K: L.41, P.43, D.93, G.94, T.95, T.96, S.97, T.161, T.162, G.410, G.411, G.412, L.451, V.480, N.481, G.482, I.495, K.502 Ligands: MG.32, AF3.33 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:G.42, K:G.94, K:G.94, K:T.95, K:T.96, K:S.97, K:T.162, K:G.411, K:G.412, K:N.481, K:G.482, K:K.502, K:K.502 Salt bridges: K:K.163, K:K.163 ADP.34: 21 residues within 4Å: Chain L: L.52, G.53, P.54, D.104, G.105, T.106, T.107, S.108, T.169, S.170, N.172, S.173, G.424, G.425, G.426, L.465, I.493, V.508, Q.510 Ligands: MG.35, AF3.36 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:G.53, L:G.105, L:T.106, L:T.107, L:T.107, L:T.107, L:S.108, L:N.172, L:S.173, L:S.173, L:G.425, L:G.426 Salt bridges: L:K.174 ADP.37: 21 residues within 4Å: Chain M: L.52, G.53, P.54, D.104, G.105, T.106, T.107, T.172, G.174, S.175, G.421, G.422, L.462, I.491, C.493, L.494, M.501, V.506, E.508 Ligands: MG.38, AF3.39 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:G.53, M:G.105, M:T.106, M:S.175, M:S.175, M:G.422, M:G.423, M:E.508 Salt bridges: M:K.176 ADP.40: 21 residues within 4Å: Chain N: 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.41, AF3.42 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.39, N:G.91, N:T.92, N:T.92, N:T.92, N:T.93, N:S.94, N:A.411, N:G.412, N:D.496 Salt bridges: N:K.159, N:K.159 ADP.43: 21 residues within 4Å: Chain O: T.39, L.40, G.41, D.92, G.93, T.94, T.95, S.96, T.161, S.164, S.165, G.408, G.409, G.410, L.449, V.477, V.492, E.494, R.499 Ligands: MG.44, AF3.45 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:G.41, O:G.93, O:T.94, O:T.94, O:T.95, O:S.96, O:S.164, O:S.164, O:S.165, O:G.409, O:G.410, O:E.494, O:R.499 Salt bridges: O:K.166 ADP.46: 18 residues within 4Å: Chain P: Y.47, G.48, P.49, D.99, G.100, T.101, N.102, F.103, M.169, S.170, G.411, G.412, L.452, L.480, I.482, I.497 Ligands: MG.47, AF3.48 9 PLIP interactions: 9 interactions with chain P Hydrogen bonds: P:Y.47, P:Y.47, P:G.48, P:D.99, P:G.100, P:N.102, P:F.103, P:S.170, P:G.412

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.88, K.159 Ligands: ADP.1, AF3.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.88 MG.5: 4 residues within 4Å: Chain B: D.97, T.166 Ligands: ADP.4, AF3.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.97 MG.8: 4 residues within 4Å: Chain C: D.93, S.159 Ligands: ADP.7, AF3.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.93, C:D.93 MG.11: 3 residues within 4Å: Chain D: D.104 Ligands: ADP.10, AF3.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.104, D:D.104 MG.14: 4 residues within 4Å: Chain E: D.104, K.176 Ligands: ADP.13, AF3.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.104 MG.17: 3 residues within 4Å: Chain F: D.90 Ligands: ADP.16, AF3.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.90, F:D.90 MG.20: 3 residues within 4Å: Chain G: D.92 Ligands: ADP.19, AF3.21 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain H: D.99, K.171 Ligands: ADP.22, AF3.24 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain I: D.88, K.159 Ligands: ADP.25, AF3.27 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.88 MG.29: 4 residues within 4Å: Chain J: D.97, T.166 Ligands: ADP.28, AF3.30 No protein-ligand interaction detected (PLIP) MG.32: 6 residues within 4Å: Chain K: D.93, S.159, T.162, K.163 Ligands: ADP.31, AF3.33 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.93 MG.35: 4 residues within 4Å: Chain L: D.104, G.105 Ligands: ADP.34, AF3.36 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.104, L:D.104 MG.38: 2 residues within 4Å: Chain M: D.104 Ligands: ADP.37 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.104 MG.41: 4 residues within 4Å: Chain N: D.90, K.159 Ligands: ADP.40, AF3.42 No protein-ligand interaction detected (PLIP) MG.44: 5 residues within 4Å: Chain O: D.92, K.166, D.391 Ligands: ADP.43, AF3.45 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.92 MG.47: 3 residues within 4Å: Chain P: S.170 Ligands: ADP.46, AF3.48 No protein-ligand interaction detected (PLIP)

16 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 9 residues within 4Å: Chain A: D.57, G.58, G.87, D.88, T.90, K.159, D.394 Ligands: ADP.1, MG.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.394 AF3.6: 9 residues within 4Å: Chain B: N.65, D.66, D.97, T.99, T.100, K.170, D.392 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) AF3.9: 9 residues within 4Å: Chain C: D.62, G.63, G.92, D.93, G.94, T.95, K.163 Ligands: ADP.7, MG.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.93 AF3.12: 8 residues within 4Å: Chain D: D.73, D.104, T.106, S.173, K.174, D.407 Ligands: ADP.10, MG.11 No protein-ligand interaction detected (PLIP) AF3.15: 9 residues within 4Å: Chain E: N.72, D.73, D.104, G.105, T.106, T.107, K.176 Ligands: ADP.13, MG.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.73 AF3.18: 11 residues within 4Å: Chain F: K.58, D.59, G.60, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.16, MG.17 No protein-ligand interaction detected (PLIP) AF3.21: 9 residues within 4Å: Chain G: N.60, D.92, G.93, T.94, T.95, K.166, D.391 Ligands: ADP.19, MG.20 No protein-ligand interaction detected (PLIP) AF3.24: 8 residues within 4Å: Chain H: D.68, A.69, D.99, T.101, K.171, D.394 Ligands: ADP.22, MG.23 No protein-ligand interaction detected (PLIP) AF3.27: 9 residues within 4Å: Chain I: D.57, G.58, G.87, T.90, T.91, K.159, D.394 Ligands: ADP.25, MG.26 No protein-ligand interaction detected (PLIP) AF3.30: 7 residues within 4Å: Chain J: D.66, D.97, T.99, T.100, K.170 Ligands: ADP.28, MG.29 No protein-ligand interaction detected (PLIP) AF3.33: 7 residues within 4Å: Chain K: D.62, D.93, G.94, T.95, K.163 Ligands: ADP.31, MG.32 No protein-ligand interaction detected (PLIP) AF3.36: 9 residues within 4Å: Chain L: N.72, D.73, D.104, T.106, S.173, K.174, D.407 Ligands: ADP.34, MG.35 No protein-ligand interaction detected (PLIP) AF3.39: 10 residues within 4Å: Chain M: N.72, D.73, G.74, D.104, G.105, T.106, T.107, K.176, D.404 Ligands: ADP.37 No protein-ligand interaction detected (PLIP) AF3.42: 11 residues within 4Å: Chain N: K.58, D.59, G.60, D.90, G.91, T.92, T.93, K.159, D.393 Ligands: ADP.40, MG.41 No protein-ligand interaction detected (PLIP) AF3.45: 8 residues within 4Å: Chain O: N.60, D.61, G.93, T.94, K.166, D.391 Ligands: ADP.43, MG.44 No protein-ligand interaction detected (PLIP) AF3.48: 7 residues within 4Å: Chain P: D.68, D.99, T.101, K.171, D.394 Ligands: ADP.46, MG.47 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roh, S.H. et al., Human TRiC-PhLP2A complex in the closed state. To Be Published

Release Date

2024-01-31

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
Phosducin-like protein 3: QR

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

Q
Q

R
R

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

Phosducin-like protein 3

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