SMTL ID : 3avi.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

SER-LEU-LYS-ILE-ASP-ASN-MET-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 15 PLIP interactions: 8 interactions with chain A, 7 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:H.142, B:T.145 Water bridges: A:T.96, A:T.96 Salt bridges: B:H.142 SER-LEU-LYS-ILE-ASP-ASN-MET-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: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:T.95, B:W.102, B:W.103, A:T.145 Hydrogen bonds: B:Q.66, B:T.96, A:Q.139, A:E.141, A:E.141, A:H.142, A:T.145 Water bridges: B:T.96, B:T.96 Salt bridges: A:H.142

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

SO4.3: 3 residues within 4Å: Chain A: T.37, H.38, K.130 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.37, A:H.38, A:N.126 Water bridges: A:T.37, A:K.130 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.137, A:L.143 Water bridges: A:K.42, A:K.42, A:E.141, 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 8 PLIP interactions: 8 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:Q.66, A:T.95 SO4.6: 6 residues within 4Å: Chain A: E.56, F.71, K.74, R.78 Chain B: R.78 Ligands: SO4.13 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.56, A:A.57, A:R.78 Salt bridges: A:K.74, B:R.78 SO4.10: 3 residues within 4Å: Chain B: T.37, H.38, K.130 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.37, B:H.38 Water bridges: B:T.37, B:N.126 Salt bridges: B:H.38, B:K.130 SO4.11: 5 residues within 4Å: Chain B: K.42, R.137, E.141, H.142, L.143 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.137, B:L.143 Water bridges: B:K.42, B:K.144 Salt bridges: B:K.42, B:H.142 SO4.12: 4 residues within 4Å: Chain B: G.65, S.94, T.95, T.96 9 PLIP interactions: 9 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.96, B:T.96 SO4.13: 6 residues within 4Å: Chain A: R.78 Chain B: E.56, F.71, K.74, R.78 Ligands: SO4.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.78, B:K.74 Hydrogen bonds: B:E.56

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

CL.7: 3 residues within 4Å: Chain A: V.43, A.62, E.63 Ligand excluded by PLIP

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

ACY.8: 8 residues within 4Å: Chain A: Y.54, N.155, H.156 Chain B: G.77, R.78, W.79, P.80 Ligands: ACY.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.155, A:H.156 Salt bridges: A:H.156 Hydrogen bonds: B:G.77 ACY.9: 7 residues within 4Å: Chain A: W.79, G.168, V.172 Chain B: R.78, W.79, P.80 Ligands: ACY.8 No protein-ligand interaction detected (PLIP) ACY.14: 8 residues within 4Å: Chain A: G.77, R.78, W.79, P.80 Chain B: N.155, H.156, G.168 Ligands: ACY.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.155 Water bridges: B:N.155, B:H.156 Salt bridges: B:H.156 ACY.15: 7 residues within 4Å: Chain A: R.78, W.79, P.80 Chain B: W.79, G.168, V.172 Ligands: ACY.14 No protein-ligand interaction detected (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

2012-02-15

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrase

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