SMTL ID : 7pux.1

Structure of p97 N-D1(L198W) in complex with Fragment TROLL2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: D.205, I.206, G.207, C.209, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409, A.412 Chain E: K.236, F.360 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.207, A:G.248, A:T.249, A:T.249, A:G.250, A:K.251, A:T.252, A:T.252, A:T.252, A:L.253, A:H.384 Water bridges: A:T.252, A:G.408, E:K.236 Salt bridges: A:K.251 ADP.21: 19 residues within 4Å: Chain B: D.205, I.206, G.207, C.209, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409, A.412 Chain F: K.236, F.360 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.207, B:G.248, B:T.249, B:T.249, B:G.250, B:K.251, B:T.252, B:T.252, B:T.252, B:L.253, B:H.384 Water bridges: B:T.252, B:G.408, F:K.236 Salt bridges: B:K.251 ADP.41: 19 residues within 4Å: Chain C: D.205, I.206, G.207, C.209, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409, A.412 Chain D: K.236, F.360 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252, C:T.252, C:L.253, C:H.384 Water bridges: C:T.252, C:G.408, D:K.236 Salt bridges: C:K.251 ADP.61: 19 residues within 4Å: Chain B: K.236, F.360 Chain D: D.205, I.206, G.207, C.209, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409, A.412 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.207, D:G.248, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252, D:T.252, D:L.253, D:H.384 Water bridges: D:T.252, D:G.408, B:K.236 Salt bridges: D:K.251 ADP.81: 19 residues within 4Å: Chain C: K.236, F.360 Chain E: D.205, I.206, G.207, C.209, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409, A.412 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:T.252, E:L.253, E:H.384 Water bridges: E:T.252, E:G.408, C:K.236 Salt bridges: E:K.251 ADP.101: 19 residues within 4Å: Chain A: K.236, F.360 Chain F: D.205, I.206, G.207, C.209, P.247, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409, A.412 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:T.252, F:T.252, F:L.253, F:H.384 Water bridges: F:T.252, F:G.408, A:K.236 Salt bridges: F:K.251

96 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 3 residues within 4Å: Chain A: Q.398, M.449, R.453 Ligand excluded by PLIP FMT.3: 8 residues within 4Å: Chain A: R.358, R.359, F.360 Chain F: P.247, G.248, V.407, A.409, R.461 Ligand excluded by PLIP FMT.4: 5 residues within 4Å: Chain A: P.137, Y.138, A.142, R.144 Ligands: FMT.13 Ligand excluded by PLIP FMT.5: 6 residues within 4Å: Chain A: R.25, K.60, G.61, V.99, I.100, S.101 Ligand excluded by PLIP FMT.6: 8 residues within 4Å: Chain A: R.86, R.89, N.90, V.94, R.95, L.96, N.260, E.261 Ligand excluded by PLIP FMT.7: 6 residues within 4Å: Chain A: H.384, M.388, C.415, S.416 Chain E: G.234, V.235 Ligand excluded by PLIP FMT.9: 6 residues within 4Å: Chain A: R.22, P.23, R.25, L.26, K.45, E.80 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain A: P.44, K.45, E.48, D.79 Ligand excluded by PLIP FMT.11: 7 residues within 4Å: Chain A: N.36, V.87, N.91, P.145, I.146, D.150, F.152 Ligand excluded by PLIP FMT.12: 9 residues within 4Å: Chain A: I.274, M.275, K.277, L.278, A.279, S.282, V.320, I.324 Chain E: R.323 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain A: P.137, Y.138, V.154, R.155 Ligands: FMT.4 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain A: K.62, K.63 Ligand excluded by PLIP FMT.15: 3 residues within 4Å: Chain A: R.256, F.266, L.268 Ligand excluded by PLIP FMT.16: 3 residues within 4Å: Chain A: K.63, R.93, E.195 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain A: V.108, K.109, Y.110 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain A: R.155, G.156, K.386, N.387, M.388, K.389 Ligand excluded by PLIP FMT.22: 3 residues within 4Å: Chain B: Q.398, M.449, R.453 Ligand excluded by PLIP FMT.23: 8 residues within 4Å: Chain B: R.358, R.359, F.360 Chain D: P.247, G.248, V.407, A.409, R.461 Ligand excluded by PLIP FMT.24: 5 residues within 4Å: Chain B: P.137, Y.138, A.142, R.144 Ligands: FMT.33 Ligand excluded by PLIP FMT.25: 6 residues within 4Å: Chain B: R.25, K.60, G.61, V.99, I.100, S.101 Ligand excluded by PLIP FMT.26: 8 residues within 4Å: Chain B: R.86, R.89, N.90, V.94, R.95, L.96, N.260, E.261 Ligand excluded by PLIP FMT.27: 6 residues within 4Å: Chain B: H.384, M.388, C.415, S.416 Chain F: G.234, V.235 Ligand excluded by PLIP FMT.29: 6 residues within 4Å: Chain B: R.22, P.23, R.25, L.26, K.45, E.80 Ligand excluded by PLIP FMT.30: 4 residues within 4Å: Chain B: P.44, K.45, E.48, D.79 Ligand excluded by PLIP FMT.31: 7 residues within 4Å: Chain B: N.36, V.87, N.91, P.145, I.146, D.150, F.152 Ligand excluded by PLIP FMT.32: 9 residues within 4Å: Chain B: I.274, M.275, K.277, L.278, A.279, S.282, V.320, I.324 Chain F: R.323 Ligand excluded by PLIP FMT.33: 5 residues within 4Å: Chain B: P.137, Y.138, V.154, R.155 Ligands: FMT.24 Ligand excluded by PLIP FMT.34: 2 residues within 4Å: Chain B: K.62, K.63 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain B: R.256, F.266, L.268 Ligand excluded by PLIP FMT.36: 3 residues within 4Å: Chain B: K.63, R.93, E.195 Ligand excluded by PLIP FMT.37: 3 residues within 4Å: Chain B: V.108, K.109, Y.110 Ligand excluded by PLIP FMT.39: 6 residues within 4Å: Chain B: R.155, G.156, K.386, N.387, M.388, K.389 Ligand excluded by PLIP FMT.42: 3 residues within 4Å: Chain C: Q.398, M.449, R.453 Ligand excluded by PLIP FMT.43: 8 residues within 4Å: Chain C: R.358, R.359, F.360 Chain E: P.247, G.248, V.407, A.409, R.461 Ligand excluded by PLIP FMT.44: 5 residues within 4Å: Chain C: P.137, Y.138, A.142, R.144 Ligands: FMT.53 Ligand excluded by PLIP FMT.45: 6 residues within 4Å: Chain C: R.25, K.60, G.61, V.99, I.100, S.101 Ligand excluded by PLIP FMT.46: 8 residues within 4Å: Chain C: R.86, R.89, N.90, V.94, R.95, L.96, N.260, E.261 Ligand excluded by PLIP FMT.47: 6 residues within 4Å: Chain C: H.384, M.388, C.415, S.416 Chain D: G.234, V.235 Ligand excluded by PLIP FMT.49: 6 residues within 4Å: Chain C: R.22, P.23, R.25, L.26, K.45, E.80 Ligand excluded by PLIP FMT.50: 4 residues within 4Å: Chain C: P.44, K.45, E.48, D.79 Ligand excluded by PLIP FMT.51: 7 residues within 4Å: Chain C: N.36, V.87, N.91, P.145, I.146, D.150, F.152 Ligand excluded by PLIP FMT.52: 9 residues within 4Å: Chain C: I.274, M.275, K.277, L.278, A.279, S.282, V.320, I.324 Chain D: R.323 Ligand excluded by PLIP FMT.53: 5 residues within 4Å: Chain C: P.137, Y.138, V.154, R.155 Ligands: FMT.44 Ligand excluded by PLIP FMT.54: 2 residues within 4Å: Chain C: K.62, K.63 Ligand excluded by PLIP FMT.55: 3 residues within 4Å: Chain C: R.256, F.266, L.268 Ligand excluded by PLIP FMT.56: 3 residues within 4Å: Chain C: K.63, R.93, E.195 Ligand excluded by PLIP FMT.57: 3 residues within 4Å: Chain C: V.108, K.109, Y.110 Ligand excluded by PLIP FMT.59: 6 residues within 4Å: Chain C: R.155, G.156, K.386, N.387, M.388, K.389 Ligand excluded by PLIP FMT.62: 3 residues within 4Å: Chain D: Q.398, M.449, R.453 Ligand excluded by PLIP FMT.63: 8 residues within 4Å: Chain C: P.247, G.248, V.407, A.409, R.461 Chain D: R.358, R.359, F.360 Ligand excluded by PLIP FMT.64: 5 residues within 4Å: Chain D: P.137, Y.138, A.142, R.144 Ligands: FMT.73 Ligand excluded by PLIP FMT.65: 6 residues within 4Å: Chain D: R.25, K.60, G.61, V.99, I.100, S.101 Ligand excluded by PLIP FMT.66: 8 residues within 4Å: Chain D: R.86, R.89, N.90, V.94, R.95, L.96, N.260, E.261 Ligand excluded by PLIP FMT.67: 6 residues within 4Å: Chain B: G.234, V.235 Chain D: H.384, M.388, C.415, S.416 Ligand excluded by PLIP FMT.69: 6 residues within 4Å: Chain D: R.22, P.23, R.25, L.26, K.45, E.80 Ligand excluded by PLIP FMT.70: 4 residues within 4Å: Chain D: P.44, K.45, E.48, D.79 Ligand excluded by PLIP FMT.71: 7 residues within 4Å: Chain D: N.36, V.87, N.91, P.145, I.146, D.150, F.152 Ligand excluded by PLIP FMT.72: 9 residues within 4Å: Chain B: R.323 Chain D: I.274, M.275, K.277, L.278, A.279, S.282, V.320, I.324 Ligand excluded by PLIP FMT.73: 5 residues within 4Å: Chain D: P.137, Y.138, V.154, R.155 Ligands: FMT.64 Ligand excluded by PLIP FMT.74: 2 residues within 4Å: Chain D: K.62, K.63 Ligand excluded by PLIP FMT.75: 3 residues within 4Å: Chain D: R.256, F.266, L.268 Ligand excluded by PLIP FMT.76: 3 residues within 4Å: Chain D: K.63, R.93, E.195 Ligand excluded by PLIP FMT.77: 3 residues within 4Å: Chain D: V.108, K.109, Y.110 Ligand excluded by PLIP FMT.79: 6 residues within 4Å: Chain D: R.155, G.156, K.386, N.387, M.388, K.389 Ligand excluded by PLIP FMT.82: 3 residues within 4Å: Chain E: Q.398, M.449, R.453 Ligand excluded by PLIP FMT.83: 8 residues within 4Å: Chain A: P.247, G.248, V.407, A.409, R.461 Chain E: R.358, R.359, F.360 Ligand excluded by PLIP FMT.84: 5 residues within 4Å: Chain E: P.137, Y.138, A.142, R.144 Ligands: FMT.93 Ligand excluded by PLIP FMT.85: 6 residues within 4Å: Chain E: R.25, K.60, G.61, V.99, I.100, S.101 Ligand excluded by PLIP FMT.86: 8 residues within 4Å: Chain E: R.86, R.89, N.90, V.94, R.95, L.96, N.260, E.261 Ligand excluded by PLIP FMT.87: 6 residues within 4Å: Chain C: G.234, V.235 Chain E: H.384, M.388, C.415, S.416 Ligand excluded by PLIP FMT.89: 6 residues within 4Å: Chain E: R.22, P.23, R.25, L.26, K.45, E.80 Ligand excluded by PLIP FMT.90: 4 residues within 4Å: Chain E: P.44, K.45, E.48, D.79 Ligand excluded by PLIP FMT.91: 7 residues within 4Å: Chain E: N.36, V.87, N.91, P.145, I.146, D.150, F.152 Ligand excluded by PLIP FMT.92: 9 residues within 4Å: Chain C: R.323 Chain E: I.274, M.275, K.277, L.278, A.279, S.282, V.320, I.324 Ligand excluded by PLIP FMT.93: 5 residues within 4Å: Chain E: P.137, Y.138, V.154, R.155 Ligands: FMT.84 Ligand excluded by PLIP FMT.94: 2 residues within 4Å: Chain E: K.62, K.63 Ligand excluded by PLIP FMT.95: 3 residues within 4Å: Chain E: R.256, F.266, L.268 Ligand excluded by PLIP FMT.96: 3 residues within 4Å: Chain E: K.63, R.93, E.195 Ligand excluded by PLIP FMT.97: 3 residues within 4Å: Chain E: V.108, K.109, Y.110 Ligand excluded by PLIP FMT.99: 6 residues within 4Å: Chain E: R.155, G.156, K.386, N.387, M.388, K.389 Ligand excluded by PLIP FMT.102: 3 residues within 4Å: Chain F: Q.398, M.449, R.453 Ligand excluded by PLIP FMT.103: 8 residues within 4Å: Chain B: P.247, G.248, V.407, A.409, R.461 Chain F: R.358, R.359, F.360 Ligand excluded by PLIP FMT.104: 5 residues within 4Å: Chain F: P.137, Y.138, A.142, R.144 Ligands: FMT.113 Ligand excluded by PLIP FMT.105: 6 residues within 4Å: Chain F: R.25, K.60, G.61, V.99, I.100, S.101 Ligand excluded by PLIP FMT.106: 8 residues within 4Å: Chain F: R.86, R.89, N.90, V.94, R.95, L.96, N.260, E.261 Ligand excluded by PLIP FMT.107: 6 residues within 4Å: Chain A: G.234, V.235 Chain F: H.384, M.388, C.415, S.416 Ligand excluded by PLIP FMT.109: 6 residues within 4Å: Chain F: R.22, P.23, R.25, L.26, K.45, E.80 Ligand excluded by PLIP FMT.110: 4 residues within 4Å: Chain F: P.44, K.45, E.48, D.79 Ligand excluded by PLIP FMT.111: 7 residues within 4Å: Chain F: N.36, V.87, N.91, P.145, I.146, D.150, F.152 Ligand excluded by PLIP FMT.112: 9 residues within 4Å: Chain A: R.323 Chain F: I.274, M.275, K.277, L.278, A.279, S.282, V.320, I.324 Ligand excluded by PLIP FMT.113: 5 residues within 4Å: Chain F: P.137, Y.138, V.154, R.155 Ligands: FMT.104 Ligand excluded by PLIP FMT.114: 2 residues within 4Å: Chain F: K.62, K.63 Ligand excluded by PLIP FMT.115: 3 residues within 4Å: Chain F: R.256, F.266, L.268 Ligand excluded by PLIP FMT.116: 3 residues within 4Å: Chain F: K.63, R.93, E.195 Ligand excluded by PLIP FMT.117: 3 residues within 4Å: Chain F: V.108, K.109, Y.110 Ligand excluded by PLIP FMT.119: 6 residues within 4Å: Chain F: R.155, G.156, K.386, N.387, M.388, K.389 Ligand excluded by PLIP

6 x 6LY: (1S)-2-amino-1-(4-bromophenyl)ethan-1-ol(Non-covalent)

6LY.8: 8 residues within 4Å: Chain A: R.113, I.114, H.115, E.167, T.168, D.169, H.183, E.185 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.115, A:H.183 Hydrogen bonds: A:H.183, A:E.185, A:E.185 pi-Stacking: A:H.115, A:H.183 Halogen bonds: A:R.113 6LY.28: 8 residues within 4Å: Chain B: R.113, I.114, H.115, E.167, T.168, D.169, H.183, E.185 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.115, B:H.183 Hydrogen bonds: B:H.183, B:E.185, B:E.185 pi-Stacking: B:H.115, B:H.183 Halogen bonds: B:R.113 6LY.48: 8 residues within 4Å: Chain C: R.113, I.114, H.115, E.167, T.168, D.169, H.183, E.185 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:H.115, C:H.183 Hydrogen bonds: C:H.183, C:E.185, C:E.185 pi-Stacking: C:H.115, C:H.183 Halogen bonds: C:R.113 6LY.68: 8 residues within 4Å: Chain D: R.113, I.114, H.115, E.167, T.168, D.169, H.183, E.185 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:H.115, D:H.183 Hydrogen bonds: D:H.183, D:E.185, D:E.185 pi-Stacking: D:H.115, D:H.183 Halogen bonds: D:R.113 6LY.88: 8 residues within 4Å: Chain E: R.113, I.114, H.115, E.167, T.168, D.169, H.183, E.185 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:H.115, E:H.183 Hydrogen bonds: E:H.183, E:E.185, E:E.185 pi-Stacking: E:H.115, E:H.183 Halogen bonds: E:R.113 6LY.108: 8 residues within 4Å: Chain F: R.113, I.114, H.115, E.167, T.168, D.169, H.183, E.185 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:H.115, F:H.183 Hydrogen bonds: F:H.183, F:E.185, F:E.185 pi-Stacking: F:H.115, F:H.183 Halogen bonds: F:R.113

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 11 residues within 4Å: Chain A: P.223, F.230, P.237, R.239, L.335, K.336, R.338, A.339, H.340, V.341, I.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.340, A:V.341 PEG.38: 11 residues within 4Å: Chain B: P.223, F.230, P.237, R.239, L.335, K.336, R.338, A.339, H.340, V.341, I.342 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.340, B:V.341 PEG.58: 11 residues within 4Å: Chain C: P.223, F.230, P.237, R.239, L.335, K.336, R.338, A.339, H.340, V.341, I.342 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.340, C:V.341 PEG.78: 11 residues within 4Å: Chain D: P.223, F.230, P.237, R.239, L.335, K.336, R.338, A.339, H.340, V.341, I.342 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.340, D:V.341 PEG.98: 11 residues within 4Å: Chain E: P.223, F.230, P.237, R.239, L.335, K.336, R.338, A.339, H.340, V.341, I.342 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.340, E:V.341 PEG.118: 11 residues within 4Å: Chain F: P.223, F.230, P.237, R.239, L.335, K.336, R.338, A.339, H.340, V.341, I.342 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.340, F:V.341

6 x NA: SODIUM ION(Non-functional Binders)

NA.20: 5 residues within 4Å: Chain A: R.191, E.192, E.194, E.195, E.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.196, A:E.196 Water bridges: A:E.196 NA.40: 5 residues within 4Å: Chain B: R.191, E.192, E.194, E.195, E.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.194, B:E.196 Water bridges: B:E.196 NA.60: 5 residues within 4Å: Chain C: R.191, E.192, E.194, E.195, E.196 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.194, C:E.196 Water bridges: C:E.196 NA.80: 5 residues within 4Å: Chain D: R.191, E.192, E.194, E.195, E.196 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.196, D:E.196 Water bridges: D:E.196 NA.100: 5 residues within 4Å: Chain E: R.191, E.192, E.194, E.195, E.196 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.196, E:E.196 Water bridges: E:E.196 NA.120: 5 residues within 4Å: Chain F: R.191, E.192, E.194, E.195, E.196 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.191, F:E.196 Water bridges: F:E.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bothe, S. et al., Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97. Commun Chem (2022)

Release Date

2022-12-14

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Transitional endoplasmic reticulum ATPase

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