SMTL ID : 5cym.1

HIV-1 reverse transcriptase complexed with 4-iodopyrazole

Coordinates

PDB Format Compare

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: 19 residues within 4Å: Chain A: P.97, L.102, K.103, K.104, K.105, V.108, V.181, Y.183, Y.185, Y.190, G.192, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.97, A:L.102, 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:W.231, A:L.236, A:Y.320 Hydrogen bonds: A:K.103, A:K.103 Water bridges: A:I.182

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

SO4.2: 5 residues within 4Å: Chain A: K.333, G.335, Q.336, G.337, K.514 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.336, A:Q.336 Salt bridges: A:K.333, A:K.514 SO4.3: 7 residues within 4Å: Chain A: R.279, Q.280, K.283, R.286, Q.336, R.358, K.514 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.280, A:R.358 Salt bridges: A:R.279, A:K.283, A:K.514 SO4.4: 4 residues within 4Å: Chain A: K.478, S.517, E.518, L.519 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.517, A:S.517, A:E.518, A:L.519 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 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.406, B:Q.332 Salt bridges: B:K.424

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

EDO.5: 10 residues within 4Å: Chain A: N.365, W.403, K.426, L.427, W.428, Y.429, Q.430, Q.511, P.512, D.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.426, A:W.428, A:Y.429, A:Y.429 EDO.6: 9 residues within 4Å: Chain A: I.7, E.8, V.10, I.161, S.164, S.165, K.168 Chain B: G.51, P.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.8, A:E.8, A:S.164 Water bridges: A:E.8 EDO.21: 5 residues within 4Å: Chain B: W.24, R.78, E.399, W.402, T.403 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.399, B:W.402 Water bridges: B:E.399, B:T.400 EDO.22: 9 residues within 4Å: Chain B: I.31, K.32, V.35, I.132, P.133, S.134, T.139, G.141, I.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.132 Water bridges: B:K.32

14 x IOD: IODIDE ION(Non-functional Binders)

IOD.7: 8 residues within 4Å: Chain A: I.7, A.116, V.120, F.162, S.165, M.166, I.169, L.216 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: L.454, G.455, K.456, P.470, L.471 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: T.364, K.514, S.515, E.516 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: G.455, K.456, S.555, A.556 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: P.249, K.261, L.262, K.265 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: T.109, H.200, R.201, I.204 Ligand excluded by PLIP IOD.13: 9 residues within 4Å: Chain A: D.445, G.446, K.456, A.457, G.458, V.468, L.553 Ligands: IOD.14, IOD.16 Ligand excluded by PLIP IOD.14: 7 residues within 4Å: Chain A: G.458, Y.459, V.460, V.468, L.553 Ligands: IOD.13, IOD.15 Ligand excluded by PLIP IOD.15: 8 residues within 4Å: Chain A: Y.443, D.445, Y.459, V.460, G.546, N.547, D.551 Ligands: IOD.14 Ligand excluded by PLIP IOD.16: 6 residues within 4Å: Chain A: D.445, G.446, A.447, D.551, S.555 Ligands: IOD.13 Ligand excluded by PLIP IOD.23: 5 residues within 4Å: Chain B: A.114, F.160, M.164, I.167, L.209 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain B: V.8, F.87, I.159 Ligand excluded by PLIP IOD.25: 6 residues within 4Å: Chain B: V.111, D.113, A.114, P.225, L.228 Ligands: IOD.26 Ligand excluded by PLIP IOD.26: 7 residues within 4Å: Chain B: L.209, L.210, W.212, G.213, P.225, L.228 Ligands: IOD.25 Ligand excluded by PLIP

6 x PYZ: 4-IODOPYRAZOLE(Non-covalent)(Covalent)

PYZ.17: 7 residues within 4Å: Chain A: T.167, L.170, E.171, A.174, I.182 Chain B: T.139, P.140 No protein-ligand interaction detected (PLIP) PYZ.18: 6 residues within 4Å: Chain A: K.22, V.23, K.24, P.57, N.59, R.145 No protein-ligand interaction detected (PLIP) PYZ.27: 9 residues within 4Å: Chain B: Y.232, E.370, Q.373, K.374, T.377, Q.407, A.408, W.410 Ligands: PYZ.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.232, B:T.377 pi-Stacking: B:Y.232 PYZ.28: 11 residues within 4Å: Chain B: L.74, V.75, D.76, F.77, R.78, N.81, G.152, M.184, T.409, W.410, I.411 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.76, B:D.76, B:F.77, B:R.78 PYZ.29: 7 residues within 4Å: Chain B: P.247, K.249, W.252, D.256, K.259, L.260, K.263 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.256, B:D.256 PYZ.30: 8 residues within 4Å: Chain B: Y.232, L.234, W.239, Y.354, K.374, T.377, E.378 Ligands: PYZ.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.239, B:Y.354 Halogen bonds: B:Y.232

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

DMS.19: 10 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.431, L.527, I.528, K.530, E.531, K.532, V.533 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.430 DMS.31: 7 residues within 4Å: Chain A: K.13, P.16, Q.87, D.88 Chain B: P.55, Y.56, K.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.126 DMS.32: 9 residues within 4Å: Chain A: T.378, I.382, T.388 Chain B: T.27, K.30, T.400, W.401, T.403, E.404 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.404 DMS.33: 8 residues within 4Å: Chain B: Q.242, P.243, I.244, I.270, V.314, N.348, T.351, Y.427 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.348 DMS.34: 12 residues within 4Å: Chain A: I.382, V.383 Chain B: Q.23, W.24, P.25, L.26, I.31, P.133, S.134, I.135, N.136, N.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauman, J.D. et al., Rapid experimental SAD phasing and hot spot identification with halogenated fragments. Iucrj (2016)

Release Date

2015-12-30

Peptides

HIV-1 reverse transcriptase, p66 subunit: A
HIV-1 reverse transcriptase, p51 subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 reverse transcriptase, p66 subunit

HIV-1 reverse transcriptase, p51 subunit

Related Entries With Identical Sequence