SMTL ID : 6cgf.1

Crystal structure of HIV-1 Y188L mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5a2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-1-1-mer

Ligands

1 x K5A: 4-[(4-{[4-(4-cyano-2,6-dimethylphenoxy)thieno[3,2-d]pyrimidin-2-yl]amino}piperidin-1-yl)methyl]benzene-1-sulfonamide(Non-covalent)

K5A.1: 21 residues within 4Å: Chain A: P.97, L.102, K.103, K.104, K.105, K.106, S.107, V.108, V.181, Y.183, L.190, V.191, G.192, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.108, A:V.181, A:Y.183, A:L.190, A:L.190, A:F.229, A:W.231, A:L.236, A:P.238 Hydrogen bonds: A:K.103, A:V.108 Water bridges: A:K.103, A:K.103

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.445, D.500, D.551 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.1, H2O.5, H2O.8, H2O.9

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: I.528 No protein-ligand interaction detected (PLIP)

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

SO4.4: 6 residues within 4Å: Chain A: M.43, K.75, F.118, Y.148, P.152, Q.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.148, A:Y.148, A:Q.153 Water bridges: A:K.75, A:Q.153, A:Q.153 Salt bridges: A:K.75 SO4.5: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.336, A:Q.336 Water bridges: A:K.333, A:D.366 Salt bridges: A:K.333, A:K.514 SO4.6: 5 residues within 4Å: Chain A: K.478, E.516, S.517, E.518, L.519 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.516, A:E.518, A:L.519 Water bridges: A:S.517 Salt bridges: A:K.478 SO4.19: 5 residues within 4Å: Chain A: Q.87 Chain B: E.53, P.55, Y.56, K.126 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.53 Salt bridges: B:K.126 SO4.20: 8 residues within 4Å: Chain A: T.405, E.406, Y.407, W.408 Chain B: K.331, Q.332, G.333, K.424 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:E.406, A:K.433, B:K.424 Hydrogen bonds: B:K.331 Salt bridges: B:K.424 SO4.21: 4 residues within 4Å: Chain B: I.274, K.275, V.276, R.277 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.542 Hydrogen bonds: B:V.276, B:R.277 SO4.22: 4 residues within 4Å: Chain B: L.234, H.235, W.239 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.235, B:H.235

23 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: K.426, L.427, W.428, Y.429, Q.511, D.513 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: L.488, S.491, G.492, L.493, Q.526, K.529, K.530 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: W.90 Chain B: K.20, V.21, K.22 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: W.90, V.92, S.164 Chain B: I.50, G.51, P.52, R.143 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: R.450, T.475, N.476, Q.477 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: E.8, K.168 Chain B: K.49, I.50, G.51 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: W.268, Q.271 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: E.398, E.401, T.402 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: R.465, D.490, S.491, G.492 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: Y.534, L.535, A.536 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: N.138, N.139 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Y.429, Q.430, L.527, K.530, E.531, K.532, V.533 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: W.24, E.399, W.402, T.403 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: V.75, F.77, R.78, N.81, G.152, W.410, I.411 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: K.65, V.108, D.110, D.186, Q.407, T.409 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: Y.232, Y.354, K.374, E.378 Ligands: SO4.22 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: T.378, I.382 Chain B: T.27, T.400, W.401, E.404 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: P.157, Y.183, M.184 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: Q.502, W.537 Chain B: W.266, Q.269, W.426 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: E.434, P.435 Chain B: T.253, N.255, D.256, K.259, L.289 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: E.28, I.135, E.138 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain B: N.348, T.351 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: W.239, T.240, V.241 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors. Elife (2018)

Release Date

2018-08-01

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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