SMTL ID : 4xfz.1

Structure of the native full-length HIV-1 capsid protein in complex with PF-3450074 (PF74)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

IOD.1: 4 residues within 4Å: Chain A: K.170, R.173 Chain F: G.60, G.61 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: S.16, P.17 Chain E: R.18 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: Q.219 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: N.21 Chain E: R.18 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain B: K.170, R.173 Chain D: G.60, G.61 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: S.16, P.17 Chain F: R.18 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain B: Q.219 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain B: N.21 Chain F: R.18 Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain C: K.170, R.173 Chain E: G.60, G.61 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain C: S.16, P.17 Chain D: R.18 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain C: Q.219 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain C: N.21 Chain D: R.18 Ligand excluded by PLIP IOD.28: 4 residues within 4Å: Chain C: G.60, G.61 Chain D: K.170, R.173 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain B: R.18 Chain D: S.16, P.17 Ligand excluded by PLIP IOD.32: 1 residues within 4Å: Chain D: Q.219 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain B: R.18 Chain D: N.21 Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain A: G.60, G.61 Chain E: K.170, R.173 Ligand excluded by PLIP IOD.38: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.40: 3 residues within 4Å: Chain C: R.18 Chain E: S.16, P.17 Ligand excluded by PLIP IOD.41: 1 residues within 4Å: Chain E: Q.219 Ligand excluded by PLIP IOD.42: 2 residues within 4Å: Chain C: R.18 Chain E: N.21 Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain B: G.60, G.61 Chain F: K.170, R.173 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.49: 3 residues within 4Å: Chain A: R.18 Chain F: S.16, P.17 Ligand excluded by PLIP IOD.50: 1 residues within 4Å: Chain F: Q.219 Ligand excluded by PLIP IOD.51: 2 residues within 4Å: Chain A: R.18 Chain F: N.21 Ligand excluded by PLIP

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

CL.7: 1 residues within 4Å: Chain E: Q.179 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: N.57 Chain E: P.38, R.173 Ligands: 1B0.9 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain F: Q.179 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: N.57 Chain F: P.38, R.173 Ligands: 1B0.18 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain D: Q.179 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: N.57 Chain D: P.38, R.173 Ligands: 1B0.27 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Chain B: Q.179 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain B: P.38, R.173 Chain D: N.57 Ligands: 1B0.36 Ligand excluded by PLIP CL.43: 1 residues within 4Å: Chain C: Q.179 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain C: P.38, R.173 Chain E: N.57 Ligands: 1B0.45 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain A: Q.179 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain A: P.38, R.173 Chain F: N.57 Ligands: 1B0.54 Ligand excluded by PLIP

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

1B0.9: 14 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, A.105, T.107, Y.130 Chain E: Y.169, R.173, K.182 Ligands: CL.8 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:N.53, A:L.56, A:L.56, A:M.66, A:L.69, A:K.70, A:A.105, A:T.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 1B0.18: 14 residues within 4Å: Chain B: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, A.105, T.107, Y.130 Chain F: Y.169, R.173, K.182 Ligands: CL.17 18 PLIP interactions: 3 interactions with chain F, 15 interactions with chain B Hydrophobic interactions: F:R.173, F:R.173, F:K.182, B:N.53, B:L.56, B:L.56, B:M.66, B:L.69, B:K.70, B:A.105, B:T.107 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 1B0.27: 14 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, A.105, T.107, Y.130 Chain D: Y.169, R.173, K.182 Ligands: CL.26 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:N.53, C:L.56, C:L.56, C:M.66, C:L.69, C:K.70, C:A.105, C:T.107, D:R.173, D:R.173, D: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 1B0.36: 14 residues within 4Å: Chain B: Y.169, R.173, K.182 Chain D: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, A.105, T.107, Y.130 Ligands: CL.35 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:N.53, D:L.56, D:L.56, D:M.66, D:L.69, D:K.70, D:A.105, D:T.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 1B0.45: 14 residues within 4Å: Chain C: Y.169, R.173, K.182 Chain E: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, A.105, T.107, Y.130 Ligands: CL.44 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:N.53, E:L.56, E:L.56, E:M.66, E:L.69, E:K.70, E:A.105, E:T.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 1B0.54: 14 residues within 4Å: Chain A: Y.169, R.173, K.182 Chain F: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, A.105, T.107, Y.130 Ligands: CL.53 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:N.53, F:L.56, F:L.56, F:M.66, F:L.69, F:K.70, F:A.105, F:T.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

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gres, A.T. et al., STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability. Science (2015)

Release Date

2015-06-10

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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