SMTL ID : 5cyq.1

HIV-1 reverse transcriptase complexed with 4-bromopyrazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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: 20 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, V.191, G.192, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.97, A:L.102, A:K.105, A:V.108, A:V.181, 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:L.230

15 x BYZ: 4-bromo-1H-pyrazole(Non-covalent)

BYZ.2: 9 residues within 4Å: Chain A: I.7, A.116, S.119, V.120, F.162, S.165, M.166, I.169, L.216 1 PLIP interactions: 1 interactions with chain A Halogen bonds: A:F.162 BYZ.3: 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) BYZ.4: 7 residues within 4Å: Chain A: Q.93, G.95, I.96, P.97, Y.183 Chain B: N.137, P.140 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:Y.183 BYZ.5: 6 residues within 4Å: Chain A: R.279, R.358, T.364, K.514, S.515, E.516 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.279, A:R.358 BYZ.6: 6 residues within 4Å: Chain A: K.22, V.23, K.24, P.57, N.59, R.145 No protein-ligand interaction detected (PLIP) BYZ.7: 5 residues within 4Å: Chain A: L.454, G.455, K.456, P.470, L.471 1 PLIP interactions: 1 interactions with chain A Halogen bonds: A:G.455 BYZ.8: 7 residues within 4Å: Chain A: D.445, G.446, A.447, K.456, A.457, V.468 Ligands: BYZ.9 No protein-ligand interaction detected (PLIP) BYZ.9: 11 residues within 4Å: Chain A: Y.443, V.444, D.445, G.458, Y.459, V.460, V.468, G.546, N.547, E.548 Ligands: BYZ.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.548 BYZ.17: 12 residues within 4Å: Chain B: V.111, D.113, A.114, F.160, M.164, I.167, L.209, L.210, W.212, G.213, P.225, L.228 No protein-ligand interaction detected (PLIP) BYZ.18: 11 residues within 4Å: Chain A: I.382, V.383 Chain B: 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:L.26 BYZ.19: 9 residues within 4Å: Chain B: Y.232, L.234, W.239, Y.354, R.356, K.374, T.377, E.378 Ligands: BYZ.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.239, B:E.378 BYZ.20: 11 residues within 4Å: Chain B: Y.232, R.358, E.370, Q.373, K.374, T.377, Q.407, A.408, W.410 Ligands: BYZ.19, BYZ.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.377 pi-Stacking: B:Y.232 BYZ.21: 7 residues within 4Å: Chain B: P.247, K.249, W.252, D.256, K.259, L.260, K.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.256, B:D.256, B:K.259 BYZ.22: 10 residues within 4Å: Chain B: K.65, V.108, D.186, Y.232, T.377, Q.407, A.408, T.409, W.410 Ligands: BYZ.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.65, B:T.409, B:T.409, B:T.409 BYZ.23: 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:V.75, B:D.76, B:F.77, B:R.78

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

DMS.10: 4 residues within 4Å: Chain A: R.450, 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.11: 6 residues within 4Å: Chain A: K.333, G.335, Q.336, G.337, D.366, K.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.336 DMS.12: 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.13: 8 residues within 4Å: Chain A: N.365, K.426, L.427, W.428, Y.429, Q.511, P.512, D.513 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.428 Salt bridges: A:D.513 pi-Cation interactions: A:Y.429 DMS.24: 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.25: 7 residues within 4Å: Chain A: K.13, P.16, Q.87 Chain B: E.53, P.55, Y.56, K.126 No protein-ligand interaction detected (PLIP) DMS.26: 9 residues within 4Å: Chain B: Q.242, P.243, I.244, V.245, K.263, W.266, W.426, Y.427, Q.428 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.263 DMS.27: 9 residues within 4Å: Chain A: Q.502, W.537 Chain B: N.265, W.266, Q.269, F.346, L.422, V.423, W.426 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.426 DMS.28: 5 residues within 4Å: Chain B: W.24, R.78, E.399, W.402, W.414 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.402 Salt bridges: B:E.399 pi-Cation interactions: B:W.24 DMS.29: 9 residues within 4Å: Chain B: W.337, Y.354, R.356, M.357, R.358, Q.367, E.370, A.371, K.374 No protein-ligand interaction detected (PLIP)

3 x BR: BROMIDE ION(Non-covalent)

BR.14: 5 residues within 4Å: Chain A: K.390, F.391, K.392, W.416, E.417 Ligand excluded by PLIP BR.15: 3 residues within 4Å: Chain A: Q.244, I.246, W.268 Ligand excluded by PLIP BR.16: 3 residues within 4Å: Chain A: M.43, K.48, F.118 Ligand excluded by PLIP

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

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