SMTL ID : 4ig3.1

HIV-1 reverse transcriptase with bound fragment near Knuckles site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x T27: 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile(Non-covalent)

T27.1: 17 residues within 4Å: Chain A: P.97, L.102, K.103, K.105, V.108, V.181, Y.183, Y.190, P.227, F.229, L.230, W.231, L.236, H.237, P.238, Y.320 Chain B: E.139 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.97, A:K.105, A:V.108, A:V.181, A:Y.183, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:W.231, A:L.236, A:Y.320 Hydrogen bonds: A:K.103, A:K.103 Water bridges: A:I.182, A:Y.190

15 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 8 residues within 4Å: Chain A: N.365, W.403, K.426, L.427, W.428, Y.429, Q.511, D.513 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.366 Salt bridges: A:D.513 DMS.3: 7 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, I.528, K.530, E.531 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: Q.502, W.537 Chain B: Q.270, L.423, W.427 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.266 DMS.5: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.514 DMS.6: 3 residues within 4Å: Chain A: T.475, N.476, Q.477 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.475, A:N.476, A:Q.477 DMS.7: 6 residues within 4Å: Chain A: P.245, I.246, Y.273, L.312, E.314, P.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.273 DMS.8: 5 residues within 4Å: Chain A: R.279, Q.280, K.283, Q.336, R.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.279, A:R.358 DMS.10: 5 residues within 4Å: Chain A: T.388 Chain B: T.28, T.401, W.402, E.405 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.405 DMS.11: 4 residues within 4Å: Chain A: Q.87 Chain B: P.56, Y.57, K.127 No protein-ligand interaction detected (PLIP) DMS.12: 9 residues within 4Å: Chain A: I.382, V.383 Chain B: P.26, L.27, I.32, P.134, S.135, I.136, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.137 DMS.13: 4 residues within 4Å: Chain B: L.235, H.236, K.239, W.240 No protein-ligand interaction detected (PLIP) DMS.14: 8 residues within 4Å: Chain B: Q.243, P.244, I.245, V.246, K.264, W.427, Y.428, Q.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.246, B:K.264 DMS.15: 3 residues within 4Å: Chain B: W.25, E.400, W.403 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.400 DMS.16: 2 residues within 4Å: Chain B: V.318, Y.319 No protein-ligand interaction detected (PLIP) DMS.17: 8 residues within 4Å: Chain A: T.405, E.406, Y.407, W.408 Chain B: K.332, Q.333, G.334, K.425 No protein-ligand interaction detected (PLIP)

1 x J94: (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium(Non-covalent)

J94.9: 10 residues within 4Å: Chain A: I.7, E.8, V.10, S.164, S.165, K.168 Chain B: K.50, I.51, G.52, P.53 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.8, A:V.10, A:K.168 Water bridges: A:E.8, A:S.165, A:K.168 Salt bridges: A:E.8, A:K.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauman, J.D. et al., Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening. J.Med.Chem. (2013)

Release Date

2013-02-06

Peptides

Reverse transcriptase/ribonuclease H: A
P51 RT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H

P51 RT

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