SMTL ID : 3avk.1

Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x SER- LEU- LYS- ILE- ASP- ASN- GLU- ASP: LEDGF peptide(Non-covalent)

SER-LEU-LYS-ILE-ASP-ASN-GLU-ASP.1: 14 residues within 4Å: Chain A: Q.66, T.95, T.96, A.99, A.100, W.102, W.103 Chain B: D.138, Q.139, A.140, E.141, H.142, T.145, M.149 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:T.95, A:A.99, A:W.102, A:W.103, B:T.145 Hydrogen bonds: A:Q.66, A:T.96, B:Q.139, B:E.141, B:E.141, B:E.141, B:H.142, B:T.145 Water bridges: A:T.96, A:T.96 Salt bridges: B:H.142 SER-LEU-LYS-ILE-ASP-ASN-GLU-ASP.2: 14 residues within 4Å: Chain A: D.138, Q.139, A.140, E.141, H.142, T.145, M.149 Chain B: Q.66, T.95, T.96, A.99, A.100, W.102, W.103 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:T.145, B:T.95, B:A.99, B:W.102, B:W.103 Hydrogen bonds: A:Q.139, A:E.141, A:E.141, A:H.142, B:Q.66, B:T.96, B:A.100 Salt bridges: A:H.142 Water bridges: B:T.96

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

SO4.3: 3 residues within 4Å: Chain A: T.37, H.38, K.130 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.38, A:N.126 Water bridges: A:T.37, A:T.37 Salt bridges: A:H.38, A:K.130 SO4.4: 5 residues within 4Å: Chain A: K.42, R.137, E.141, H.142, L.143 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.144 Salt bridges: A:K.42, A:H.142 SO4.5: 4 residues within 4Å: Chain A: G.65, S.94, T.95, T.96 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.65, A:S.94, A:T.95, A:T.96, A:T.96 Water bridges: A:Q.66, A:T.96 SO4.6: 7 residues within 4Å: Chain A: E.56, A.57, F.71, K.74, R.78 Chain B: R.78 Ligands: SO4.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.56, A:E.56, A:A.57 Salt bridges: A:K.74, B:R.78 SO4.9: 3 residues within 4Å: Chain B: T.37, H.38, K.130 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.37, B:T.37, B:H.38 Salt bridges: B:H.38, B:K.130 SO4.10: 4 residues within 4Å: Chain B: K.42, R.137, H.142, L.143 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.144 Salt bridges: B:K.42, B:H.142 SO4.11: 5 residues within 4Å: Chain B: G.65, Q.66, S.94, T.95, T.96 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.65, B:Q.66, B:S.94, B:T.95, B:T.96, B:T.96 Water bridges: B:Q.66, B:T.95 SO4.12: 9 residues within 4Å: Chain A: R.78 Chain B: E.56, A.57, E.58, F.71, K.74, L.75, R.78 Ligands: SO4.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.56, B:E.56, B:A.57, B:E.58, B:E.58 Salt bridges: B:K.74, A:R.78

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 9 residues within 4Å: Chain A: A.76, G.77, R.78, W.79, P.80 Chain B: Y.54, N.155, H.156, G.168 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.156 Hydrogen bonds: A:G.77 ACY.13: 9 residues within 4Å: Chain A: Y.54, N.155, H.156, G.168 Chain B: A.76, G.77, R.78, W.79, P.80 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.54, A:N.155 Salt bridges: A:H.156 Hydrogen bonds: B:G.77 Water bridges: B:V.81

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

CL.8: 3 residues within 4Å: Chain A: V.43, A.62, E.63 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: V.43, A.62, E.63 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rhodes, D.I. et al., Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site. Chembiochem (2011)

Release Date

2012-01-18

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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