SMTL ID : 1exq.1

CRYSTAL STRUCTURE OF THE HIV-1 INTEGRASE CATALYTIC CORE DOMAIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.10, H.12, E.37 Ligands: CD.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:H.12, A:E.37, A:E.37 CD.2: 5 residues within 4Å: Chain A: C.10, E.37, D.61 Ligands: CD.1, CL.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.10, A:E.37, A:D.61, H2O.1 CD.5: 4 residues within 4Å: Chain B: C.10, H.12, E.37 Ligands: CD.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.10, B:H.12, B:E.37 CD.6: 5 residues within 4Å: Chain B: C.10, E.37, D.61 Ligands: CD.5, CL.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.10, B:E.37, B:D.61, H2O.3, H2O.3

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

CL.3: 5 residues within 4Å: Chain A: C.10, L.19, N.65, F.66 Ligands: CD.2 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: C.10, L.19, N.65, F.66 Ligands: CD.6 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: K.16, R.111, E.115, H.116, L.117 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.111, A:E.115, A:L.117 Salt bridges: A:K.16, A:H.116 SO4.8: 6 residues within 4Å: Chain B: K.16, R.111, E.115, H.116, L.117, K.118 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.115, B:L.117 Salt bridges: B:K.16, B:H.116, B:K.118 SO4.9: 6 residues within 4Å: Chain A: T.119, M.123 Chain B: L.47, A.73, A.74, W.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.73 SO4.10: 6 residues within 4Å: Chain A: L.47, A.73, A.74, W.77 Chain B: T.119, M.123 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J.C. et al., Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc.Natl.Acad.Sci.USA (2000)

Release Date

2000-11-03

Peptides

POL POLYPROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL POLYPROTEIN