SMTL ID : 7sr6.2 (1 other biounit)

Human Endogenous Retrovirus (HERV-K) reverse transcriptase ternary complex with dsDNA template Primer and dNTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

18 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.1: 4 residues within 4Å: Chain A: P.510, Y.511, V.520, L.568 Ligand excluded by PLIP DIO.3: 5 residues within 4Å: Chain A: L.426, K.428, V.431, I.452, D.453 Ligand excluded by PLIP DIO.4: 5 residues within 4Å: Chain A: I.436, G.439, Q.442 Chain B: Y.396 Ligands: DIO.23 Ligand excluded by PLIP DIO.9: 4 residues within 4Å: Chain A: T.476, R.477, C.478, R.547 Ligand excluded by PLIP DIO.10: 4 residues within 4Å: Chain A: P.357, N.417, D.418, D.420 Ligand excluded by PLIP DIO.11: 5 residues within 4Å: Chain A: P.128, S.129, P.130, T.302, E.381 Ligand excluded by PLIP DIO.12: 5 residues within 4Å: Chain A: W.382, S.383, F.384 Chain C: A.9, A.10 Ligand excluded by PLIP DIO.13: 5 residues within 4Å: Chain A: P.306, L.339, V.340, K.343, F.464 Ligand excluded by PLIP DIO.14: 7 residues within 4Å: Chain A: P.134, W.137, S.209, D.210, C.211, Y.212, P.354 Ligand excluded by PLIP DIO.16: 4 residues within 4Å: Chain A: G.81, H.82, P.152, V.181 Ligand excluded by PLIP DIO.17: 3 residues within 4Å: Chain A: L.467, T.468, W.470 Ligand excluded by PLIP DIO.18: 3 residues within 4Å: Chain A: R.477, C.478, E.479 Ligand excluded by PLIP DIO.19: 6 residues within 4Å: Chain A: I.475, R.576, N.577, F.578, P.579 Ligands: EDO.15 Ligand excluded by PLIP DIO.23: 8 residues within 4Å: Chain A: G.439, Q.442 Chain B: Y.396, L.397, I.400, P.425, L.426 Ligands: DIO.4 Ligand excluded by PLIP DIO.25: 3 residues within 4Å: Chain B: G.405, R.408, L.409 Ligand excluded by PLIP DIO.26: 4 residues within 4Å: Chain B: Q.375, N.376, T.377, D.378 Ligand excluded by PLIP DIO.27: 2 residues within 4Å: Chain B: D.320, S.321 Ligand excluded by PLIP DIO.28: 6 residues within 4Å: Chain B: A.347, T.377, D.378, L.379, I.461, F.462 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.143, L.144, D.218 Ligands: TTP.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.143, A:D.143, A:L.144, A:D.218 MG.33: 5 residues within 4Å: Chain B: R.111, N.114, V.449, G.450, I.451 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:R.111, B:V.449, B:G.450

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.5: 15 residues within 4Å: Chain A: K.99, R.105, D.143, L.144, K.145, D.146, C.147, F.148, Q.184, D.218, K.252 Chain C: A.4, C.5 Chain D: G.20 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.148, A:Q.184 Hydrogen bonds: A:D.146, A:C.147, A:F.148, A:Q.184 Water bridges: A:G.185 Salt bridges: A:K.99, A:K.99, A:R.105, A:R.105, A:K.252, A:K.252, A:K.252

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

EDO.6: 6 residues within 4Å: Chain A: H.71, A.74, N.75, L.78, T.175, F.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.175, A:T.175 EDO.7: 4 residues within 4Å: Chain A: Q.527, D.530, K.575, N.577 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.527, A:K.575, A:N.577 EDO.8: 2 residues within 4Å: Chain A: P.425, N.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.454 EDO.15: 4 residues within 4Å: Chain A: R.574, R.576, N.577 Ligands: DIO.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.576 EDO.29: 4 residues within 4Å: Chain A: T.589 Chain B: N.297, R.300, T.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.297, B:R.300, B:T.307

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: K.280, I.471 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.21: 3 residues within 4Å: Chain A: Q.124, Q.194 Chain C: T.7 No protein-ligand interaction detected (PLIP) K.22: 1 residues within 4Å: Chain A: F.393 No protein-ligand interaction detected (PLIP) K.31: 1 residues within 4Å: Chain B: W.56 No protein-ligand interaction detected (PLIP) K.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.24: 6 residues within 4Å: Chain B: Q.359, K.421, I.451, D.453, H.455, P.457 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baldwin, E.T. et al., Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-07-20

Peptides

Polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

Polymerase

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