SMTL ID : 6axv.1

Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-hexamer

Ligands

30 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 4 residues within 4Å: Chain A: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: K.170, R.173 Chain F: G.61 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: M.144 Chain E: Q.219 Ligands: CL.70 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: Q.179 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: P.38, S.41 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain B: K.170, R.173 Chain D: G.61 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain B: M.144 Chain F: Q.219 Ligands: CL.85 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain B: Q.179 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain B: P.38, S.41 Ligand excluded by PLIP IOD.31: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain C: K.170, R.173 Chain E: G.61 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain C: M.144 Chain D: Q.219 Ligands: CL.55 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain C: Q.179 Ligand excluded by PLIP IOD.35: 2 residues within 4Å: Chain C: P.38, S.41 Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.47: 3 residues within 4Å: Chain C: G.61 Chain D: K.170, R.173 Ligand excluded by PLIP IOD.48: 3 residues within 4Å: Chain B: Q.219 Chain D: M.144 Ligands: CL.25 Ligand excluded by PLIP IOD.49: 1 residues within 4Å: Chain D: Q.179 Ligand excluded by PLIP IOD.50: 2 residues within 4Å: Chain D: P.38, S.41 Ligand excluded by PLIP IOD.61: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.62: 3 residues within 4Å: Chain A: G.61 Chain E: K.170, R.173 Ligand excluded by PLIP IOD.63: 3 residues within 4Å: Chain C: Q.219 Chain E: M.144 Ligands: CL.40 Ligand excluded by PLIP IOD.64: 1 residues within 4Å: Chain E: Q.179 Ligand excluded by PLIP IOD.65: 2 residues within 4Å: Chain E: P.38, S.41 Ligand excluded by PLIP IOD.76: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.77: 3 residues within 4Å: Chain B: G.61 Chain F: K.170, R.173 Ligand excluded by PLIP IOD.78: 3 residues within 4Å: Chain A: Q.219 Chain F: M.144 Ligands: CL.10 Ligand excluded by PLIP IOD.79: 1 residues within 4Å: Chain F: Q.179 Ligand excluded by PLIP IOD.80: 2 residues within 4Å: Chain F: P.38, S.41 Ligand excluded by PLIP

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

CL.6: 2 residues within 4Å: Chain F: N.57 Ligands: 1B0.90 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: P.17 Chain E: R.18 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.18 Chain F: P.17 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: I.129 Ligands: CL.12 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: F.161, R.162, M.215, C.218, Q.219 Ligands: IOD.78 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: Q.176, A.177, S.178 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: P.125 Ligands: CL.9 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: I.153, R.167 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: A.31, F.32, Y.145 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain D: N.57 Ligands: 1B0.60 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: P.17 Chain F: R.18 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: R.18 Chain D: P.17 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: I.129 Ligands: CL.27 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain B: F.161, R.162, M.215, C.218, Q.219 Ligands: IOD.48 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: Q.176, A.177, S.178 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: P.125 Ligands: CL.24 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: I.153, R.167 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: A.31, F.32, Y.145 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain E: N.57 Ligands: 1B0.75 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain C: P.17 Chain D: R.18 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain C: R.18 Chain E: P.17 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain C: I.129 Ligands: CL.42 Ligand excluded by PLIP CL.40: 6 residues within 4Å: Chain C: F.161, R.162, M.215, C.218, Q.219 Ligands: IOD.63 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain C: Q.176, A.177, S.178 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain C: P.125 Ligands: CL.39 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain C: I.153, R.167 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain C: A.31, F.32, Y.145 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain C: N.57 Ligands: 1B0.45 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain B: R.18 Chain D: P.17 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain C: P.17 Chain D: R.18 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain D: I.129 Ligands: CL.57 Ligand excluded by PLIP CL.55: 6 residues within 4Å: Chain D: F.161, R.162, M.215, C.218, Q.219 Ligands: IOD.33 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain D: Q.176, A.177, S.178 Ligand excluded by PLIP CL.57: 2 residues within 4Å: Chain D: P.125 Ligands: CL.54 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain D: I.153, R.167 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain D: A.31, F.32, Y.145 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain A: N.57 Ligands: 1B0.15 Ligand excluded by PLIP CL.67: 2 residues within 4Å: Chain C: R.18 Chain E: P.17 Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain A: P.17 Chain E: R.18 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain E: I.129 Ligands: CL.72 Ligand excluded by PLIP CL.70: 6 residues within 4Å: Chain E: F.161, R.162, M.215, C.218, Q.219 Ligands: IOD.3 Ligand excluded by PLIP CL.71: 3 residues within 4Å: Chain E: Q.176, A.177, S.178 Ligand excluded by PLIP CL.72: 2 residues within 4Å: Chain E: P.125 Ligands: CL.69 Ligand excluded by PLIP CL.73: 2 residues within 4Å: Chain E: I.153, R.167 Ligand excluded by PLIP CL.74: 3 residues within 4Å: Chain E: A.31, F.32, Y.145 Ligand excluded by PLIP CL.81: 2 residues within 4Å: Chain B: N.57 Ligands: 1B0.30 Ligand excluded by PLIP CL.82: 2 residues within 4Å: Chain A: R.18 Chain F: P.17 Ligand excluded by PLIP CL.83: 2 residues within 4Å: Chain B: P.17 Chain F: R.18 Ligand excluded by PLIP CL.84: 2 residues within 4Å: Chain F: I.129 Ligands: CL.87 Ligand excluded by PLIP CL.85: 6 residues within 4Å: Chain F: F.161, R.162, M.215, C.218, Q.219 Ligands: IOD.18 Ligand excluded by PLIP CL.86: 3 residues within 4Å: Chain F: Q.176, A.177, S.178 Ligand excluded by PLIP CL.87: 2 residues within 4Å: Chain F: P.125 Ligands: CL.84 Ligand excluded by PLIP CL.88: 2 residues within 4Å: Chain F: I.153, R.167 Ligand excluded by PLIP CL.89: 3 residues within 4Å: Chain F: A.31, F.32, Y.145 Ligand excluded by PLIP

6 x 1B0: N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE(Non-covalent)

1B0.15: 14 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, I.107, Y.130 Chain E: Y.169, L.172, R.173, K.182 Ligands: CL.66 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:L.56, A:L.56, A:M.66, A:K.70, A:A.105, A:I.107, A:I.107, E:R.173, E:R.173, E:K.182 Hydrogen bonds: A:N.57, A:N.57, A:Q.63, A:K.70 pi-Cation interactions: A:K.70, A:K.70, A:K.70 1B0.30: 14 residues within 4Å: Chain B: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, I.107, Y.130 Chain F: Y.169, L.172, R.173, K.182 Ligands: CL.81 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:L.56, B:L.56, B:M.66, B:K.70, B:A.105, B:I.107, B:I.107, F:R.173, F:R.173, F:K.182 Hydrogen bonds: B:N.57, B:N.57, B:Q.63, B:K.70 pi-Cation interactions: B:K.70, B:K.70, B:K.70 1B0.45: 14 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, I.107, Y.130 Chain D: Y.169, L.172, R.173, K.182 Ligands: CL.51 17 PLIP interactions: 3 interactions with chain D, 14 interactions with chain C Hydrophobic interactions: D:R.173, D:R.173, D:K.182, C:L.56, C:L.56, C:M.66, C:K.70, C:A.105, C:I.107, C:I.107 Hydrogen bonds: C:N.57, C:N.57, C:Q.63, C:K.70 pi-Cation interactions: C:K.70, C:K.70, C:K.70 1B0.60: 14 residues within 4Å: Chain B: Y.169, L.172, R.173, K.182 Chain D: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, I.107, Y.130 Ligands: CL.21 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.56, D:L.56, D:M.66, D:K.70, D:A.105, D:I.107, D:I.107, B:R.173, B:R.173, B:K.182 Hydrogen bonds: D:N.57, D:N.57, D:Q.63, D:K.70 pi-Cation interactions: D:K.70, D:K.70, D:K.70 1B0.75: 14 residues within 4Å: Chain C: Y.169, L.172, R.173, K.182 Chain E: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, I.107, Y.130 Ligands: CL.36 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:L.56, E:L.56, E:M.66, E:K.70, E:A.105, E:I.107, E:I.107, C:R.173, C:R.173, C:K.182 Hydrogen bonds: E:N.57, E:N.57, E:Q.63, E:K.70 pi-Cation interactions: E:K.70, E:K.70, E:K.70 1B0.90: 14 residues within 4Å: Chain A: Y.169, L.172, R.173, K.182 Chain F: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, I.107, Y.130 Ligands: CL.6 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:L.56, F:L.56, F:M.66, F:K.70, F:A.105, F:I.107, F:I.107, A:R.173, A:R.173, A:K.182 Hydrogen bonds: F:N.57, F:N.57, F:Q.63, F:K.70 pi-Cation interactions: F:K.70, F:K.70, F:K.70

Links

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Citation

Novikova, M. et al., Identification of a novel element in HIV-1 capsid critical for assembly and maturation. To be published

Release Date

2018-09-12

Peptides

HIV-1 capsid protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

HIV-1 capsid protein

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