SMTL ID : 6dt1.1 (1 other biounit)

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: K.46, D.47, E.49, K.52, V.145, W.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.46, A:E.49 Water bridges: A:K.52 GOL.2: 4 residues within 4Å: Chain A: Y.161, Y.355, K.387, V.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.389 GOL.3: 4 residues within 4Å: Chain A: Y.400, R.403, N.424 Chain D: G.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.424 Water bridges: A:P.401 GOL.4: 5 residues within 4Å: Chain A: R.190, E.230, L.307, V.308, Y.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.190, A:R.190 GOL.5: 7 residues within 4Å: Chain A: R.202, R.379, K.385 Chain C: G.1, T.2 Ligands: DTT.12, AMP.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.202, A:R.202, A:R.379, A:R.379, A:K.385 GOL.7: 5 residues within 4Å: Chain A: L.83, E.109, G.112, Y.113, D.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.116 GOL.8: 8 residues within 4Å: Chain A: S.427, G.428, L.429, R.442 Chain C: C.3, G.4 Chain D: G.8, A.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.427, A:G.428, A:R.442, A:R.442 GOL.9: 4 residues within 4Å: Chain A: R.317, L.374, E.376, N.382 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.317, A:R.317, A:L.374, A:N.382 GOL.10: 3 residues within 4Å: Chain A: G.209, G.287, I.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.289, A:I.289 GOL.11: 5 residues within 4Å: Chain A: G.434, V.435, R.444, E.447, N.448 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.434, A:R.444 Water bridges: A:S.437 GOL.14: 6 residues within 4Å: Chain A: Q.64, K.68, R.131 Chain B: C.8 Ligands: CL.16, DTT.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.64, A:K.68, A:K.68, A:R.131 Water bridges: A:R.61 GOL.15: 4 residues within 4Å: Chain A: S.138, V.139 Chain D: C.7, G.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.138

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 17 residues within 4Å: Chain A: Y.65, Y.66, I.67, L.96, R.99, T.102, G.103, A.106, N.282, K.286 Chain B: G.7, C.8, G.9 Chain D: G.14, C.15, A.16, T.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.103, A:N.282, A:N.282, A:K.286 Water bridges: A:L.96, A:L.101

5 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)(Non-functional Binders)

DTT.12: 6 residues within 4Å: Chain A: R.61, R.202, A.203 Chain B: T.10, C.11 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.61 DTT.13: 3 residues within 4Å: Chain A: N.448, Y.451, Y.452 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.448, A:Y.452 DTT.18: 6 residues within 4Å: Chain B: C.8, G.9, T.10 Chain D: C.13 Ligands: GOL.14, DTT.21 No protein-ligand interaction detected (PLIP) DTT.20: 6 residues within 4Å: Chain A: T.35 Chain C: C.7, T.8 Chain D: G.4, T.5, C.6 No protein-ligand interaction detected (PLIP) DTT.21: 4 residues within 4Å: Chain A: R.403 Chain D: G.11, A.12 Ligands: DTT.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.403

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

CL.16: 2 residues within 4Å: Chain A: R.61 Ligands: GOL.14 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 5 residues within 4Å: Chain A: G.182, E.237 Chain B: C.11 Chain C: G.1 Ligands: AMP.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.237, H2O.2, H2O.8

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.19: 18 residues within 4Å: Chain A: L.157, Q.177, L.178, K.179, A.180, R.184, R.202, E.237, W.302, I.340, I.367, K.369, K.385, K.387 Chain C: G.1, T.2 Ligands: GOL.5, MG.17 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.177, A:A.180, A:R.184, A:R.202, A:K.369 Water bridges: A:K.179, A:R.379 Salt bridges: A:K.179, A:K.385, A:K.387 pi-Stacking: A:W.302, A:W.302, A:W.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Nucleic Acids Res. (2018)

Release Date

2018-09-19

Peptides

DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase

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