SMTL ID : 7sr6.1 (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

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain A: D.143, L.144, D.218 Ligands: DCP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.143, A:L.144, A:D.218 MG.12: 6 residues within 4Å: Chain A: T.489, D.490, E.518, S.537, D.538, N.599 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.489, A:E.518 MG.30: 1 residues within 4Å: Chain C: A.23 No protein-ligand interaction detected (PLIP)

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.2: 16 residues within 4Å: Chain A: K.99, R.105, D.143, L.144, K.145, D.146, C.147, F.148, Q.184, I.217, D.218, K.252 Chain C: G.3, A.4 Chain D: T.21 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.148, A:Q.184 Hydrogen bonds: A:L.144, A:D.146, A:C.147, A:F.148, A:Q.184 Salt bridges: A:K.99, A:K.99, A:K.99, A:R.105, A:R.105, A:K.252 pi-Cation interactions: A:R.105

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

DIO.3: 8 residues within 4Å: Chain A: V.424, L.426, T.427, K.428, V.431, I.452, D.453, N.454 Ligand excluded by PLIP DIO.4: 6 residues within 4Å: Chain A: K.474, I.475, R.477, N.577, F.578, P.579 Ligand excluded by PLIP DIO.5: 2 residues within 4Å: Chain A: P.510, L.568 Ligand excluded by PLIP DIO.6: 7 residues within 4Å: Chain A: H.367, T.468, W.470, T.551, A.552, L.553, R.574 Ligand excluded by PLIP DIO.7: 6 residues within 4Å: Chain A: P.134, S.209, D.210, C.211, Y.212 Chain B: K.171 Ligand excluded by PLIP DIO.13: 4 residues within 4Å: Chain B: I.97, Q.98, G.439, I.443 Ligand excluded by PLIP DIO.14: 7 residues within 4Å: Chain A: G.439, Q.442 Chain B: Y.396, L.397, I.400, L.426 Ligands: DIO.15 Ligand excluded by PLIP DIO.15: 6 residues within 4Å: Chain A: I.436 Chain B: A.364, T.365, A.366, Y.396 Ligands: DIO.14 Ligand excluded by PLIP DIO.16: 3 residues within 4Å: Chain A: P.592, G.593 Chain B: R.318 Ligand excluded by PLIP DIO.18: 5 residues within 4Å: Chain B: G.405, R.408, I.443, G.444, A.446 Ligand excluded by PLIP DIO.19: 4 residues within 4Å: Chain B: Q.375, N.376, T.377, D.378 Ligand excluded by PLIP DIO.20: 6 residues within 4Å: Chain B: K.291, A.364, T.365, K.466, L.467, T.468 Ligand excluded by PLIP DIO.21: 6 residues within 4Å: Chain B: T.302, L.303, K.343, S.346, A.347, I.461 Ligand excluded by PLIP DIO.22: 7 residues within 4Å: Chain B: Q.77, F.149, T.150, W.179, L.182, Q.184 Ligands: EDO.25 Ligand excluded by PLIP DIO.23: 5 residues within 4Å: Chain B: I.45, L.47, I.151, I.192, F.196 Ligand excluded by PLIP DIO.24: 3 residues within 4Å: Chain B: Q.184, N.188, N.447 Ligand excluded by PLIP

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

EDO.8: 2 residues within 4Å: Chain A: F.435 Chain B: T.394 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.394 EDO.25: 3 residues within 4Å: Chain B: Q.77, K.80 Ligands: DIO.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.77, B:Q.77, B:K.80

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

K.9: 1 residues within 4Å: Chain A: Y.541 No protein-ligand interaction detected (PLIP) K.10: 1 residues within 4Å: Chain A: G.198 No protein-ligand interaction detected (PLIP) K.11: 2 residues within 4Å: Chain A: H.387, I.554 No protein-ligand interaction detected (PLIP) K.26: 1 residues within 4Å: Chain B: W.56 No protein-ligand interaction detected (PLIP) K.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.28: 3 residues within 4Å: Chain A: Q.124, Q.194 Chain C: C.6 No protein-ligand interaction detected (PLIP) K.29: 2 residues within 4Å: Chain C: A.10, A.11 No protein-ligand interaction detected (PLIP)

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

PG6.17: 8 residues within 4Å: Chain B: Q.359, I.374, N.376, K.421, D.453, H.455, Y.456, 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
A

B
B

Polymerase

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