SMTL ID : 3wnf.1

Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x ACE- CYS- LYS- ILE- ASP- ASN- CYS- NH2: CKIDNC peptide(Non-covalent)

ACE-CYS-LYS-ILE-ASP-ASN-CYS-NH2.1: 13 residues within 4Å: Chain A: D.112, Q.113, A.114, E.115, H.116, T.119, M.123 Chain B: Q.40, A.69, T.70, A.73, W.77 Ligands: SO4.14 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:W.77, A:T.119 Hydrogen bonds: B:Q.40, B:T.70, B:T.70, A:D.112, A:Q.113, A:E.115, A:E.115, A:H.116 Water bridges: A:T.119 Salt bridges: A:H.116 ACE-CYS-LYS-ILE-ASP-ASN-CYS-NH2.2: 13 residues within 4Å: Chain A: Q.40, A.69, T.70, A.73, W.77 Chain B: D.112, Q.113, A.114, E.115, H.116, T.119, M.123 Ligands: SO4.8 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.119, A:W.77 Hydrogen bonds: B:D.112, B:Q.113, B:E.115, B:E.115, B:H.116, B:T.119, B:T.119, A:Q.40, A:T.70, A:T.70, A:T.70 Water bridges: B:T.119 Salt bridges: B:H.116

4 x CD: CADMIUM ION(Non-covalent)

CD.3: 5 residues within 4Å: Chain A: C.10, E.37, D.61 Ligands: CD.4, CL.5 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.4: 4 residues within 4Å: Chain A: C.10, H.12, E.37 Ligands: CD.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.10, A:H.12, A:E.37, A:E.37 CD.9: 4 residues within 4Å: Chain B: C.10, H.12, E.37 Ligands: CD.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.10, B:H.12, B:E.37, B:E.37 CD.10: 5 residues within 4Å: Chain B: C.10, E.37, D.61 Ligands: CD.9, CL.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.10, B:E.37, B:D.61, H2O.4

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

CL.5: 7 residues within 4Å: Chain A: C.10, L.19, E.37, D.61, N.65, F.66 Ligands: CD.3 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: C.10, L.19, E.37, D.61, N.65, F.66 Ligands: CD.10 Ligand excluded by PLIP

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

SO4.6: 4 residues within 4Å: Chain A: K.16, R.111, H.116, L.117 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.111, A:L.117 Water bridges: A:K.16, A:K.16, A:K.118 Salt bridges: A:K.16, A:H.116 SO4.7: 3 residues within 4Å: Chain A: T.11, H.12, K.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.11, A:H.12, A:N.100 Salt bridges: A:K.104 SO4.8: 7 residues within 4Å: Chain A: G.39, Q.40, G.68, A.69, T.70, V.71 Ligands: ACE-CYS-LYS-ILE-ASP-ASN-CYS-NH2.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.40, A:A.69, A:T.70, A:T.70, A:V.71 Water bridges: A:G.39, A:G.39, A:G.39, A:G.68 SO4.12: 4 residues within 4Å: Chain B: K.16, R.111, H.116, L.117 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.111, B:L.117 Water bridges: B:K.16, B:K.16, B:K.118 Salt bridges: B:K.16, B:H.116 SO4.13: 4 residues within 4Å: Chain B: T.11, H.12, N.100, K.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.12, B:N.100 Salt bridges: B:K.104 SO4.14: 7 residues within 4Å: Chain B: G.39, Q.40, G.68, A.69, T.70, V.71 Ligands: ACE-CYS-LYS-ILE-ASP-ASN-CYS-NH2.1 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.69, B:T.70, B:V.71 Water bridges: B:G.39, B:G.39, B:Q.40, B:G.68, B:G.68

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

2013-12-25

Peptides

Gag-Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gag-Pol polyprotein

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