SMTL ID : 4idk.1

HIV-1 reverse transcriptase with bound fragment at the 428 site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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 16 PLIP interactions: 16 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

1 x 1FE: N-(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)glycinamide(Non-covalent)

1FE.2: 8 residues within 4Å: Chain A: E.398, T.399, T.402, L.427, Q.430, E.432, E.531 Ligands: DMS.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.427, A:Q.430 Hydrogen bonds: A:T.402, A:T.402, A:Q.430, A:Q.430, A:E.432 Water bridges: A:T.399, A:L.427, A:E.432

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.14, H2O.14, H2O.16

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

DMS.4: 8 residues within 4Å: Chain A: N.365, W.403, K.426, L.427, W.428, Y.429, Q.511, D.513 Ligand excluded by PLIP DMS.5: 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.6: 8 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, I.528, K.530, E.531 Ligands: 1FE.2 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 Ligand excluded by PLIP DMS.8: 3 residues within 4Å: Chain A: T.475, N.476, Q.477 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: Y.117, F.118, L.151, Q.153, S.158, F.162 Ligand excluded by PLIP DMS.10: 2 residues within 4Å: Chain A: K.240, H.317 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: E.440, R.465, D.490, S.491, G.492 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: R.279, Q.280, K.283, Q.336, R.358 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: I.382, T.388 Chain B: T.28, T.401, W.402, E.405 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: K.13, Q.87 Chain B: P.56, Y.57, K.127 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: 4 residues within 4Å: Chain B: N.266, Q.270, L.423, W.427 Ligand excluded by PLIP DMS.18: 8 residues within 4Å: Chain B: Q.243, P.244, I.245, V.246, K.264, W.427, Y.428, Q.429 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: Q.243, I.245, Y.272, N.349 Ligand excluded by PLIP

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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