SMTL ID : 7mkc.1

N74D mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

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

1B0.1: 12 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, T.107, Y.130 Chain F: Y.169, R.173, K.182 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:L.56, A:M.66, A:K.70, A:T.107, F:R.173, F: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 1B0.8: 12 residues within 4Å: Chain B: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, T.107, Y.130 Chain D: Y.169, R.173, K.182 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:L.56, B:M.66, B:K.70, B:T.107, D:R.173, D: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 1B0.15: 12 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, T.107, Y.130 Chain E: Y.169, R.173, K.182 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:L.56, C:M.66, C:K.70, C:T.107, E:R.173, E:K.182 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 1B0.22: 12 residues within 4Å: Chain C: Y.169, R.173, K.182 Chain D: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, T.107, Y.130 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.56, D:M.66, D:K.70, D:T.107, C:R.173, C: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 1B0.29: 12 residues within 4Å: Chain A: Y.169, R.173, K.182 Chain E: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, T.107, Y.130 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:L.56, E:M.66, E:K.70, E:T.107, A:R.173, A: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 1B0.36: 12 residues within 4Å: Chain B: Y.169, R.173, K.182 Chain F: N.53, L.56, N.57, Q.63, M.66, K.70, A.105, T.107, Y.130 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:L.56, F:M.66, F:K.70, F:T.107, B:R.173, B: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

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

IOD.2: 5 residues within 4Å: Chain A: E.35, K.170, R.173 Chain E: G.60, G.61 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: F.161, R.162, M.215 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain F: I.37 Ligand excluded by PLIP IOD.7: 5 residues within 4Å: Chain A: M.118, P.125, V.126, G.127, E.128 Ligand excluded by PLIP IOD.9: 5 residues within 4Å: Chain B: E.35, K.170, R.173 Chain F: G.60, G.61 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: F.161, R.162, M.215 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain D: I.37 Ligand excluded by PLIP IOD.14: 5 residues within 4Å: Chain B: M.118, P.125, V.126, G.127, E.128 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain C: E.35, K.170, R.173 Chain D: G.60, G.61 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain C: F.161, R.162, M.215 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain C: P.17, R.18 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain E: I.37 Ligand excluded by PLIP IOD.21: 5 residues within 4Å: Chain C: M.118, P.125, V.126, G.127, E.128 Ligand excluded by PLIP IOD.23: 5 residues within 4Å: Chain B: G.60, G.61 Chain D: E.35, K.170, R.173 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain D: F.161, R.162, M.215 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain C: I.37 Ligand excluded by PLIP IOD.28: 5 residues within 4Å: Chain D: M.118, P.125, V.126, G.127, E.128 Ligand excluded by PLIP IOD.30: 5 residues within 4Å: Chain C: G.60, G.61 Chain E: E.35, K.170, R.173 Ligand excluded by PLIP IOD.31: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain E: F.161, R.162, M.215 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain E: P.17, R.18 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain A: I.37 Ligand excluded by PLIP IOD.35: 5 residues within 4Å: Chain E: M.118, P.125, V.126, G.127, E.128 Ligand excluded by PLIP IOD.37: 5 residues within 4Å: Chain A: G.60, G.61 Chain F: E.35, K.170, R.173 Ligand excluded by PLIP IOD.38: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.39: 3 residues within 4Å: Chain F: F.161, R.162, M.215 Ligand excluded by PLIP IOD.40: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP IOD.41: 1 residues within 4Å: Chain B: I.37 Ligand excluded by PLIP IOD.42: 5 residues within 4Å: Chain F: M.118, P.125, V.126, G.127, E.128 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selyutina, A. et al., TRIM5alpha Restriction of HIV-1-N74D Viruses in Lymphocytes Is Caused by a Loss of Cyclophilin A Protection. Viruses (2022)

Release Date

2022-05-04

Peptides

capsid protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

capsid protein

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