SMTL ID : 4y1d.1

Cyclic hexapeptide cyc[NdPopPKID] in complex with HIV-1 integrase core domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

1 x LYS- NLE- ASP- ASN- DVA- 45W: Cyclic hexapeptide cyc[NdPopPKID](Non-covalent)

LYS-NLE-ASP-ASN-DVA-45W.1: 10 residues within 4Å: Chain A: Q.123, A.124, E.125, H.126, T.129 Chain B: Q.50, L.57, T.80, A.84, W.87 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.122, A:Q.123, A:E.125, A:H.126, A:T.129, A:T.129, B:Q.50, B:Q.50 Salt bridges: A:H.126 Hydrophobic interactions: B:L.57, B:W.87, B:W.87

4 x CD: CADMIUM ION(Non-covalent)

CD.2: 4 residues within 4Å: Chain A: C.20, H.22, E.47 Ligands: CD.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.20, A:H.22, A:E.47 CD.3: 5 residues within 4Å: Chain A: C.20, E.47, D.71 Ligands: CD.2, CL.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.20, A:E.47, A:D.71, H2O.1 CD.7: 4 residues within 4Å: Chain B: C.20, H.22, E.47 Ligands: CD.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.20, B:H.22, B:E.47 CD.8: 5 residues within 4Å: Chain B: C.20, E.47, D.71 Ligands: CD.7, CL.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.20, B:E.47, B:D.71, H2O.3

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

CL.4: 7 residues within 4Å: Chain A: C.20, L.29, E.47, D.71, N.75, F.76 Ligands: CD.3 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain B: C.20, L.29, E.47, D.71, N.75, F.76 Ligands: CD.8 Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: K.26, H.126, L.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.121, A:L.127 Water bridges: A:K.128 Salt bridges: A:K.26, A:H.126 SO4.6: 3 residues within 4Å: Chain A: C.20, T.21, H.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.20, A:H.22 Salt bridges: A:H.22 SO4.10: 6 residues within 4Å: Chain B: E.24, K.26, R.121, E.125, H.126, L.127 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.125, B:L.127 Water bridges: B:K.128 Salt bridges: B:K.26, B:R.121, B:H.126 SO4.11: 4 residues within 4Å: Chain B: C.20, T.21, H.22, K.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.21, B:T.21, B:H.22 Salt bridges: B:K.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Northfield, S.E. et al., HEXAPEPTIDE MIMETICS OF LEDGF IN COMPLEX WITH HIV-1 INTEGRASE. To Be Published

Release Date

2015-05-13

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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