SMTL ID : 6aya.1

Structure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-6-6-mer

Ligands

42 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: 2 residues within 4Å: Chain A: E.35, R.173 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: M.144 Chain I: R.162, M.215 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: R.18 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.173, K.182 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: S.16, P.17, R.18 Chain I: R.18 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain C: E.35, R.173 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain C: M.144 Chain K: R.162, M.215 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain C: R.18 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain C: R.173, K.182 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain C: S.16, P.17, R.18 Chain K: R.18 Ligand excluded by PLIP IOD.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain E: E.35, R.173 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain E: M.144 Chain G: R.162, M.215 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Chain E: R.18 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain E: R.173, K.182 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain E: S.16, P.17, R.18 Chain G: R.18 Ligand excluded by PLIP IOD.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.28: 4 residues within 4Å: Chain G: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain G: E.35, R.173 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain C: R.162, M.215 Chain G: M.144 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain G: R.18 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain G: R.173, K.182 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain C: R.18 Chain G: S.16, P.17, R.18 Ligand excluded by PLIP IOD.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain I: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.38: 2 residues within 4Å: Chain I: E.35, R.173 Ligand excluded by PLIP IOD.39: 3 residues within 4Å: Chain E: R.162, M.215 Chain I: M.144 Ligand excluded by PLIP IOD.40: 1 residues within 4Å: Chain I: R.18 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain I: R.173, K.182 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain E: R.18 Chain I: S.16, P.17, R.18 Ligand excluded by PLIP IOD.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain K: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.47: 2 residues within 4Å: Chain K: E.35, R.173 Ligand excluded by PLIP IOD.48: 3 residues within 4Å: Chain A: R.162, M.215 Chain K: M.144 Ligand excluded by PLIP IOD.49: 1 residues within 4Å: Chain K: R.18 Ligand excluded by PLIP IOD.50: 2 residues within 4Å: Chain K: R.173, K.182 Ligand excluded by PLIP IOD.51: 4 residues within 4Å: Chain A: R.18 Chain K: S.16, P.17, R.18 Ligand excluded by PLIP IOD.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

CL.8: 2 residues within 4Å: Chain A: F.161, R.162 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: I.153, R.167 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: F.161, R.162 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: I.153, R.167 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain E: F.161, R.162 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain E: I.153, R.167 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain G: F.161, R.162 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain G: I.153, R.167 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain I: F.161, R.162 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain I: I.153, R.167 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain K: F.161, R.162 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain K: I.153, R.167 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gres, A.T. et al., Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Nat Commun (2023)

Release Date

2018-09-12

Peptides

HIV-1 capsid protein: ACEGIK
Nuclear pore complex protein Nup153: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
B

D
B

F
B

H
B

J
B

L
B

HIV-1 capsid protein

Nuclear pore complex protein Nup153

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