SMTL ID : 4id5.1

HIV-1 reverse transcriptase with bound fragment at the RNase H primer grip site

Coordinates

PDB Format

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: 16 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, W.231, L.236, H.237, P.238, Y.320 Chain B: E.139 18 PLIP interactions: 18 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.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

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

DMS.2: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 Ligand excluded by PLIP DMS.3: 7 residues within 4Å: Chain A: W.403, K.426, L.427, W.428, Y.429, Q.511, D.513 Ligand excluded by PLIP DMS.4: 7 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, I.528, K.530, E.531 Ligand excluded by PLIP DMS.5: 5 residues within 4Å: Chain A: R.74, K.75, Y.148, P.152, Q.153 Ligand excluded by PLIP DMS.6: 4 residues within 4Å: Chain A: R.450, T.475, N.476, Q.477 Ligand excluded by PLIP DMS.7: 7 residues within 4Å: Chain A: T.405, E.406, W.408 Chain B: K.332, Q.333, G.334, K.425 Ligand excluded by PLIP DMS.8: 3 residues within 4Å: Chain A: S.324, K.325, D.326 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: T.378, T.388 Chain B: T.28, T.401, W.402, E.405 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: Q.87 Chain B: P.56, Y.57, K.127 Ligand excluded by PLIP DMS.13: 10 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, N.138 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain B: W.338, Y.355, R.357, M.358, Q.368 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain B: L.235, H.236, W.240 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain B: W.25, E.400, W.403, T.404 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain B: N.266, Q.270, W.427 Ligand excluded by PLIP DMS.18: 7 residues within 4Å: Chain B: P.244, I.245, V.246, K.264, W.427, Y.428, Q.429 Ligand excluded by PLIP DMS.19: 6 residues within 4Å: Chain B: I.245, I.271, Y.272, V.315, N.349, T.352 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain A: T.167, L.170, E.171, A.174, I.182 Chain B: T.140, P.141 Ligand excluded by PLIP

1 x 1FF: 1-methyl-5-phenyl-1H-pyrazole-4-carboxylic acid(Non-covalent)

1FF.9: 7 residues within 4Å: Chain A: L.471, K.478, Q.482, Y.485, E.518, L.519, Q.522 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.471, A:Q.482, A:Y.485 Hydrogen bonds: A:Q.482 Water bridges: A:K.478 Salt bridges: A:K.478

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain A: D.445, D.500, D.551 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.7, H2O.8, H2O.18

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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