SMTL ID : 6zee.1

Structure of PP1(7-300) bound to Phactr1 (507-580) at pH8.4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-6-6-mer

Ligands

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 8 residues within 4Å: Chain A: D.63, D.91, N.123, H.124, H.172, H.247 Ligands: MN.2, SO4.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.91, A:H.172, A:H.247 MN.2: 9 residues within 4Å: Chain A: D.63, H.65, D.91, R.95, H.124, H.172, Y.271 Ligands: MN.1, SO4.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.63, A:H.65, A:D.91, H2O.1 MN.14: 7 residues within 4Å: Chain B: D.91, N.123, H.124, H.172, H.247 Ligands: MN.15, SO4.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.91, B:H.172, B:H.247, H2O.4 MN.15: 7 residues within 4Å: Chain B: D.63, H.65, D.91, H.124, H.172 Ligands: MN.14, SO4.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.63, B:H.65, B:D.91, H2O.4 MN.22: 7 residues within 4Å: Chain C: D.91, N.123, H.124, H.172, H.247 Ligands: MN.23, SO4.37 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.91, C:H.172, C:H.247, H2O.8 MN.23: 8 residues within 4Å: Chain C: D.63, H.65, D.91, R.95, H.172, H.247 Ligands: MN.22, SO4.37 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.63, C:H.65, C:D.91, H2O.8, H2O.8 MN.39: 7 residues within 4Å: Chain D: D.91, N.123, H.124, H.172, H.247 Ligands: MN.40, SO4.56 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.91, D:H.172, D:H.247, H2O.11 MN.40: 9 residues within 4Å: Chain D: D.63, H.65, D.91, H.172, H.247, F.266 Ligands: MN.39, EDO.46, SO4.56 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.63, D:H.65, D:D.91, H2O.11, H2O.11 MN.57: 8 residues within 4Å: Chain E: D.63, D.91, N.123, H.124, H.172, H.247 Ligands: MN.58, SO4.61 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.91, E:H.172, E:H.247, H2O.16 MN.58: 7 residues within 4Å: Chain E: D.63, H.65, D.91, H.124, F.266 Ligands: MN.57, SO4.61 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.63, E:H.65, E:D.91, H2O.16 MN.68: 8 residues within 4Å: Chain F: D.63, D.91, N.123, H.124, H.172, H.247 Ligands: MN.69, SO4.76 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.91, F:H.172, F:H.247, H2O.20 MN.69: 8 residues within 4Å: Chain F: D.63, H.65, D.91, H.124, H.172, F.266 Ligands: MN.68, SO4.76 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.63, F:H.65, F:D.91, H2O.20

54 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: L.15, V.27, Q.28, L.29, I.34, L.100, E.101, C.104, R.142, Y.143 Ligand excluded by PLIP EDO.4: 11 residues within 4Å: Chain A: I.12, L.16, F.80, P.81, P.82, Y.109, K.112, Y.113 Chain B: P.177, W.215, F.224 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: P.57, L.58, K.59, S.84, N.85, S.283, V.284, D.285 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: R.131, I.132, Y.136, D.137 Chain G: P.39, W.40, L.43, I.51 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: P.195, D.196, Q.197 Chain G: H.71, L.72, T.73, R.74, F.75 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain A: I.188, P.195, Q.197, G.198, L.199, L.200, C.201 Chain G: H.71, L.72 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: S.181, M.182, E.183, R.186, H.238 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: N.270, G.273 Chain G: Y.32, D.33, R.34, R.35 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain B: E.17 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: R.131, I.132, Y.136, D.137 Chain L: P.39, W.40, L.43, I.51 Ligand excluded by PLIP EDO.18: 9 residues within 4Å: Chain B: D.207, P.208, R.245, Q.248, V.250, E.255, F.256, F.257, T.264 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: Q.180, S.181, M.182, E.183, R.186, H.238 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain B: Q.19, G.20, S.21, Y.69, L.72, R.73, E.76 Chain L: Q.30 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain C: I.12, L.16, F.80, P.81, P.82, Y.109, K.112, Y.113 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain C: S.181, M.182, E.183, R.186, H.238 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain C: P.208, R.245, Q.248, V.250, E.255, F.256, F.257, T.264 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: Q.19, G.20, Y.69, D.70, L.72, R.73, E.76 Chain I: Q.30 Ligand excluded by PLIP EDO.28: 10 residues within 4Å: Chain C: L.15, V.27, Q.28, L.29, I.34, L.100, E.101, C.104, R.142, Y.143 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain C: R.131, I.132, Y.136, D.137 Chain I: P.39, W.40, L.43, I.51 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain C: D.207, E.217, N.218, D.219, R.220, T.225, Q.248 Ligands: EDO.35 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain C: P.57, L.58, K.59, S.84, N.85, S.283, V.284, D.285 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: R.95, R.220, Y.271 Ligands: SO4.37 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain C: P.195, D.196, Q.197 Chain I: H.71, L.72, T.73, R.74, F.75 Ligand excluded by PLIP EDO.34: 11 residues within 4Å: Chain C: R.95, G.96, K.97, Y.133, G.134, D.137 Chain I: A.36, D.37, K.38, P.39, W.40 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: D.209, V.212, E.217, D.219, T.225 Ligands: EDO.30 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain C: N.26, Q.28, R.142 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain D: I.12, L.16, F.80, P.81, P.82, Y.109, K.112, Y.113 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain D: T.30, N.32, E.33 Ligand excluded by PLIP EDO.43: 10 residues within 4Å: Chain D: L.15, V.27, Q.28, L.29, I.34, L.100, E.101, C.104, R.142, Y.143 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain D: S.181, M.182, E.183, R.186, H.238 Ligand excluded by PLIP EDO.45: 9 residues within 4Å: Chain D: R.131, I.132, Y.136, D.137 Chain J: P.39, W.40, L.43, I.51 Ligands: EDO.55 Ligand excluded by PLIP EDO.46: 9 residues within 4Å: Chain D: R.95, R.220, H.247, Q.248, V.249, F.266, Y.271 Ligands: MN.40, SO4.56 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain D: L.46, Q.48, P.49, I.50, R.190 Ligands: 16P.47 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain D: Q.48, P.49, L.52, E.53, L.54, E.115, F.118 Ligand excluded by PLIP EDO.50: 9 residues within 4Å: Chain D: R.131, Y.136, I.145, W.148, K.149 Chain J: I.51, E.54, L.55, F.58 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain D: D.209, V.212, E.217, D.219 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain D: D.196, C.201, G.221, V.222, S.223 Chain J: R.74 Ligands: GOL.82 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain D: P.195, D.196, Q.197 Chain J: H.71, L.72, T.73, R.74 Ligand excluded by PLIP EDO.54: 8 residues within 4Å: Chain D: R.95, N.123, H.124, I.129, Y.133, W.205, R.220 Ligands: SO4.56 Ligand excluded by PLIP EDO.55: 8 residues within 4Å: Chain D: R.131, Y.136 Chain J: L.43, D.47, A.50, I.51, E.54 Ligands: EDO.45 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain E: E.217, N.218, D.219, G.221 Chain F: N.7, S.10, R.14 Ligand excluded by PLIP EDO.60: 1 residues within 4Å: Chain E: E.17 Ligand excluded by PLIP EDO.63: 8 residues within 4Å: Chain E: R.131, I.132, Y.136, D.137 Chain K: P.39, W.40, L.43, I.51 Ligand excluded by PLIP EDO.64: 8 residues within 4Å: Chain E: D.209, D.211, V.212, G.216, E.217, D.219, T.225 Chain F: E.17 Ligand excluded by PLIP EDO.65: 8 residues within 4Å: Chain E: S.128, I.129, I.132 Chain K: I.51, R.52, L.55, H.76 Ligands: EDO.84 Ligand excluded by PLIP EDO.66: 9 residues within 4Å: Chain E: P.208, D.209, R.245, Q.248, V.250, E.255, F.256, F.257, T.264 Ligand excluded by PLIP EDO.67: 10 residues within 4Å: Chain E: L.15, V.27, Q.28, L.29, I.34, L.100, E.101, C.104, R.142, Y.143 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain F: F.257, A.258, K.259, R.260 Ligand excluded by PLIP EDO.72: 8 residues within 4Å: Chain F: R.131, I.132, Y.136, D.137 Chain H: P.39, W.40, L.43, I.51 Ligand excluded by PLIP EDO.73: 7 residues within 4Å: Chain F: Q.48, P.49, L.52, E.53, L.54, E.115, F.118 Ligand excluded by PLIP EDO.74: 7 residues within 4Å: Chain F: P.195, D.196, Q.197 Chain H: H.71, L.72, T.73, R.74 Ligand excluded by PLIP EDO.80: 7 residues within 4Å: Chain C: S.128, I.132 Chain I: K.48, I.51, R.52, L.55, H.76 Ligand excluded by PLIP EDO.84: 10 residues within 4Å: Chain E: S.128, I.129, V.194, P.195, D.196, W.205, V.222 Chain K: R.74, H.76 Ligands: EDO.65 Ligand excluded by PLIP EDO.86: 9 residues within 4Å: Chain B: S.128, I.129, V.194, P.195, D.196, W.205, V.222 Chain L: R.74, H.76 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 10 residues within 4Å: Chain A: S.128, I.129, V.194, P.195, D.196, C.201, W.205, V.222 Chain G: R.74, H.76 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:R.74, G:R.74, A:W.205 GOL.71: 11 residues within 4Å: Chain E: Q.213 Chain F: V.18, Q.19, G.20, S.21, P.23, Y.69, L.72, R.73, E.76 Chain H: Q.30 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 2 interactions with chain H Hydrogen bonds: F:V.18, F:G.20, F:E.76, E:Q.213, H:Q.30, H:Q.30 GOL.75: 6 residues within 4Å: Chain F: L.46, I.50, R.186, I.188, M.189, R.190 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:L.46, F:R.186, F:R.190 Water bridges: F:R.190 GOL.78: 9 residues within 4Å: Chain F: S.128, I.129, V.194, P.195, D.196, W.205, V.222 Chain H: R.74, H.76 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain H Hydrogen bonds: F:P.195, H:R.74, H:R.74, H:H.76 Water bridges: F:S.128 GOL.79: 10 residues within 4Å: Chain C: C.126, S.128, I.129, V.194, P.195, D.196, C.201, W.205, V.222 Chain I: R.74 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain I Hydrogen bonds: C:V.194, C:W.205, I:R.74, I:R.74 Water bridges: C:S.128 GOL.82: 10 residues within 4Å: Chain D: S.128, I.129, V.194, P.195, D.196, C.201, W.205, V.222 Chain J: R.74 Ligands: EDO.52 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain J Hydrogen bonds: D:W.205, J:R.74, J:R.74

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

SO4.12: 10 residues within 4Å: Chain A: H.65, D.91, R.95, N.123, H.124, R.220, H.247, Y.271 Ligands: MN.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.123, A:H.247 Salt bridges: A:H.65, A:R.95, A:H.124, A:R.220, A:H.247 SO4.13: 3 residues within 4Å: Chain A: E.17 Chain B: E.217, D.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.217, B:D.219 SO4.21: 10 residues within 4Å: Chain B: H.65, D.91, R.95, N.123, H.124, R.220, H.247, Y.271 Ligands: MN.14, MN.15 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.123, B:Y.271 Water bridges: B:R.95, B:R.220, B:R.220 Salt bridges: B:H.65, B:R.95, B:H.124, B:R.220, B:H.247 SO4.37: 11 residues within 4Å: Chain C: H.65, D.91, R.95, N.123, H.124, R.220, H.247, Y.271 Ligands: MN.22, MN.23, EDO.32 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.123, C:H.247 Water bridges: C:Y.271, C:Y.271 Salt bridges: C:H.65, C:R.95, C:H.124, C:R.220, C:H.247 SO4.38: 6 residues within 4Å: Chain C: F.257, A.258, K.259, R.260 Chain E: K.97 Chain K: D.37 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain K Hydrogen bonds: C:A.258, C:K.259, K:D.37 Water bridges: C:R.260, C:R.260 SO4.56: 12 residues within 4Å: Chain D: H.65, D.91, R.95, N.123, H.124, R.220, H.247, Y.271 Ligands: MN.39, MN.40, EDO.46, EDO.54 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.123, D:Y.271 Water bridges: D:D.91 Salt bridges: D:H.65, D:R.95, D:H.124, D:R.220, D:H.247 SO4.61: 10 residues within 4Å: Chain E: H.65, D.91, R.95, N.123, H.124, R.220, H.247, Y.271 Ligands: MN.57, MN.58 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.123 Salt bridges: E:H.65, E:R.95, E:H.124, E:R.220, E:H.247 SO4.62: 7 residues within 4Å: Chain A: K.97 Chain E: F.257, A.258, K.259, R.260 Chain G: A.36, D.37 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: E:A.258, E:K.259, G:D.37 Salt bridges: A:K.97 SO4.76: 10 residues within 4Å: Chain F: H.65, D.91, R.95, N.123, H.124, R.220, H.247, Y.271 Ligands: MN.68, MN.69 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.123 Salt bridges: F:H.65, F:R.95, F:H.124, F:R.220, F:H.247 SO4.77: 4 residues within 4Å: Chain G: R.52, R.74, H.76, R.77 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:H.76, G:R.77 Water bridges: G:R.74 Salt bridges: G:R.74, G:R.77 SO4.81: 4 residues within 4Å: Chain I: R.52, R.74, H.76, R.77 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:R.77 Salt bridges: I:R.74, I:H.76, I:R.77 SO4.83: 4 residues within 4Å: Chain J: R.52, R.74, H.76, R.77 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:R.77 Salt bridges: J:R.74, J:H.76, J:R.77 SO4.85: 5 residues within 4Å: Chain F: S.5 Chain K: R.52, R.74, H.76, R.77 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain F Hydrogen bonds: K:R.77, F:S.5 Salt bridges: K:R.74, K:H.76, K:R.77 SO4.87: 4 residues within 4Å: Chain L: R.52, R.74, H.76, R.77 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:R.77 Salt bridges: L:R.74, L:H.76, L:R.77

1 x 16P: 3,6,9,12,15,18-HEXAOXAICOSANE(Non-covalent)

16P.47: 10 residues within 4Å: Chain D: L.46, Q.48, P.49, I.50, L.51, R.186, I.188, M.189, R.190 Ligands: EDO.48 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.190, D:R.190, D:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedoryshchak, R.O. et al., Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme. Elife (2020)

Release Date

2020-09-30

Peptides

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit: ABCDEF
Phosphatase and actin regulator: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
Q

C
B

D
A

E
I

F
K

G
W

H
X

I
D

J
C

K
U

L
V

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Phosphatase and actin regulator

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