SMTL ID : 7ook.1

Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 1 residues within 4Å: Chain A: N.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.51 NA.6: 3 residues within 4Å: Chain B: N.199, N.200, F.203 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.221 NA.7: 3 residues within 4Å: Chain B: D.143, N.146, D.149 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.149, A:D.136 NA.18: 3 residues within 4Å: Chain C: D.143, N.146, D.149 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.136, C:D.143 NA.21: 2 residues within 4Å: Chain C: N.199, N.200 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.199

10 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 6 residues within 4Å: Chain A: A.123, K.124, Y.172, S.173, R.346 Ligands: MPD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.172 Water bridges: A:S.173, A:S.173 MPD.3: 9 residues within 4Å: Chain A: Y.172, D.176, R.283, L.285, R.346, D.347, P.349, F.380 Ligands: MPD.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.349 MPD.4: 9 residues within 4Å: Chain A: Q.41, T.44, T.231, Y.233 Chain B: N.304, Y.305, K.318, L.319, D.320 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.305, B:K.318 Hydrogen bonds: A:Q.41, A:Y.233 MPD.8: 7 residues within 4Å: Chain B: Y.172, D.176, L.285, R.346, D.347, P.349, F.380 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.172 Hydrogen bonds: B:R.346 MPD.9: 2 residues within 4Å: Chain B: K.189, R.191 No protein-ligand interaction detected (PLIP) MPD.10: 4 residues within 4Å: Chain B: N.79, A.221, D.222, E.224 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.79 MPD.11: 10 residues within 4Å: Chain B: E.261, S.263, V.276, Q.277, Y.278, A.279, Y.282, Y.284, Y.377, Y.379 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.261 Hydrogen bonds: B:A.279, B:Y.284, B:Y.284 MPD.15: 6 residues within 4Å: Chain C: A.123, K.124, Y.172, S.173, R.346 Ligands: MPD.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.124 MPD.19: 10 residues within 4Å: Chain C: Q.107, R.108, H.109, E.111, L.257, N.259, E.261, Y.282, Y.379, T.381 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:R.108, C:E.111 Hydrogen bonds: C:Q.107, C:R.108, C:R.108 Water bridges: C:R.108 MPD.20: 8 residues within 4Å: Chain C: Y.172, D.176, L.285, R.346, D.347, P.349, F.380 Ligands: MPD.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.172 Hydrogen bonds: C:Y.172, C:Y.172

3 x Z80: 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine(Non-covalent)

Z80.5: 17 residues within 4Å: Chain A: P.37, V.38, I.39, K.66, L.69, F.129, L.130, W.167, S.173, E.174, S.235 Chain B: R.317, L.319, T.323, A.326, Q.327, R.330 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.326, B:Q.327, A:I.39, A:L.69 pi-Cation interactions: B:R.330 Salt bridges: A:E.174 pi-Stacking: A:W.167, A:W.167 Z80.14: 16 residues within 4Å: Chain B: P.37, I.39, K.66, L.69, F.129, L.130, W.167, S.173, E.174, S.235 Chain C: R.317, L.319, T.323, A.326, Q.327, R.330 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B pi-Cation interactions: C:R.330 Hydrophobic interactions: B:I.39, B:L.69 Water bridges: B:K.66 Salt bridges: B:E.174 pi-Stacking: B:W.167, B:W.167 Z80.16: 15 residues within 4Å: Chain A: L.319, T.323, A.326, Q.327, R.330 Chain C: P.37, I.39, K.66, L.69, F.129, L.130, W.167, S.173, E.174, S.235 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.39, C:L.69, C:W.167, C:E.174 Hydrogen bonds: C:K.66 Salt bridges: C:E.174 pi-Stacking: C:W.167, C:W.167 pi-Cation interactions: A:R.330

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain B: F.47, D.48, N.51, R.52 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: R.317, Q.327, R.331, C.343, D.344 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: F.47, D.48, N.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duyvesteyn, H.M.E. et al., Bacteriophage PRD1 as a nanoscaffold for drug loading. Nanoscale (2021)

Release Date

2022-06-08

Peptides

Major capsid protein P3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

Major capsid protein P3

Related Entries With Identical Sequence