SMTL ID : 3nte.2 (1 other biounit)

Crystal Structure of the Wild-type Full-Length HIV-1 Capsid Protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

IOD.1: 2 residues within 4Å: Chain A: S.178, V.181 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Ligands: IOD.9, FE.22 Ligand excluded by PLIP IOD.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: P.1, I.15, D.51 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.173, K.182 Ligand excluded by PLIP IOD.6: 5 residues within 4Å: Chain A: G.156, P.157, K.158, E.159 Ligands: FE.18 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Ligands: FE.20 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: N.74 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: I.129, R.132 Ligands: IOD.2 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: I.37 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Ligands: FE.24, FE.26 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: P.125 Ligands: FE.26 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain B: N.5, I.6 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain B: S.178 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain B: 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: H.62, A.64, A.65 Ligand excluded by PLIP

2 x I3M: Tri-iodode Anion(Non-covalent)

I3M.13: 5 residues within 4Å: Chain A: V.27, F.32, V.36, L.138, V.142 No protein-ligand interaction detected (PLIP) I3M.32: 5 residues within 4Å: Chain B: F.32, V.36, V.59, H.62, V.142 No protein-ligand interaction detected (PLIP)

23 x FE: FE (III) ION(Non-covalent)(Non-functional Binders)

FE.14: 1 residues within 4Å: Chain A: I.2 No protein-ligand interaction detected (PLIP) FE.15: 2 residues within 4Å: Chain A: Q.112, I.115 No protein-ligand interaction detected (PLIP) FE.16: 5 residues within 4Å: Chain A: M.118, P.125, V.126, G.127, E.128 No protein-ligand interaction detected (PLIP) FE.17: 4 residues within 4Å: Chain A: E.35 Chain B: P.34, V.142, S.146 No protein-ligand interaction detected (PLIP) FE.18: 1 residues within 4Å: Ligands: IOD.6 No protein-ligand interaction detected (PLIP) FE.19: 2 residues within 4Å: Chain A: N.53, N.57 No protein-ligand interaction detected (PLIP) FE.20: 2 residues within 4Å: Chain A: P.125 Ligands: IOD.7 No protein-ligand interaction detected (PLIP) FE.21: 2 residues within 4Å: Chain A: V.142, R.143 No protein-ligand interaction detected (PLIP) FE.22: 1 residues within 4Å: Ligands: IOD.2 No protein-ligand interaction detected (PLIP) FE.23: 3 residues within 4Å: Chain A: I.15, S.16, T.19 No protein-ligand interaction detected (PLIP) FE.24: 2 residues within 4Å: Chain A: E.98 Ligands: IOD.11 No protein-ligand interaction detected (PLIP) FE.25: 2 residues within 4Å: Chain A: H.87, R.97 No protein-ligand interaction detected (PLIP) FE.26: 3 residues within 4Å: Chain A: W.80 Ligands: IOD.11, IOD.12 No protein-ligand interaction detected (PLIP) FE.33: 2 residues within 4Å: Chain B: E.71, N.74 No protein-ligand interaction detected (PLIP) FE.34: 5 residues within 4Å: Chain B: M.118, P.125, V.126, G.127, E.128 No protein-ligand interaction detected (PLIP) FE.35: 1 residues within 4Å: Chain B: R.162 No protein-ligand interaction detected (PLIP) FE.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE.37: 1 residues within 4Å: Chain B: M.118 No protein-ligand interaction detected (PLIP) FE.38: 3 residues within 4Å: Chain B: Y.169, K.170, R.173 No protein-ligand interaction detected (PLIP) FE.39: 1 residues within 4Å: Chain B: R.132 No protein-ligand interaction detected (PLIP) FE.40: 5 residues within 4Å: Chain B: S.44, E.45, G.46, E.128, K.131 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.128 FE.41: 3 residues within 4Å: Chain B: P.160, G.220, V.221 No protein-ligand interaction detected (PLIP) FE.42: 1 residues within 4Å: Chain B: I.124 No protein-ligand interaction detected (PLIP)

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

NA.43: 3 residues within 4Å: Chain B: N.74, A.77, S.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, S. et al., Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding. J.Mol.Biol. (2011)

Release Date

2010-12-01

Peptides

HIV-1 capsid protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 capsid protein

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