SMTL ID : 8v1u.1

Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x G- DT- DC- DG- DG- DA- DC: DNA/RNA (5'-R(P*G)-D(P*TP*CP*GP*GP*AP*C)-3')(Non-covalent)

G-DT-DC-DG-DG-DA-DC.1: 30 residues within 4Å: Chain A: S.46, A.47, R.48, R.292, K.311, R.332, K.487, K.489, Y.492, K.513, T.541, G.542, F.543, S.544, D.545, E.546, A.615, R.617 Chain B: C.11 Chain C: G.1, T.2, C.3, C.4, G.5, A.6, C.7, G.8 Ligands: MES.3, AMP.8, NA.9 45 PLIP interactions: 45 interactions with chain A Hydrophobic interactions: A:R.514 Hydrogen bonds: A:R.48, A:R.48, A:R.194, A:L.195, A:G.196, A:L.197, A:A.198, A:Q.200, A:S.201, A:S.201, A:Q.379, A:T.382, A:R.511, A:K.513, A:K.513, A:K.538, A:S.593, A:S.595, A:S.595, A:Y.598, A:S.612 Water bridges: A:R.192, A:R.194, A:R.300, A:S.482, A:S.482, A:S.482, A:H.483, A:R.514, A:R.514, A:R.514, A:R.514, A:K.538, A:K.538, A:G.540, A:T.541, A:T.541, A:A.615 Salt bridges: A:R.192, A:K.247, A:R.481, A:R.511, A:K.538, A:K.538

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: M.223, A.226, K.230, W.238, E.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.230

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 5 residues within 4Å: Chain A: V.45, S.46, A.47, R.50 Ligands: G-DT-DC-DG-DG-DA-DC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.46, A:S.46, A:S.46, A:A.47 MES.4: 6 residues within 4Å: Chain A: Q.103, T.163, A.164, I.167 Chain C: A.16, G.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.103 Water bridges: A:A.164

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

CL.5: 5 residues within 4Å: Chain A: R.620, V.621, R.622, E.623, D.624 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: E.89, G.91 Chain B: G.7, C.8 Chain C: A.13, T.14 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: Q.315, S.331, E.335, N.337 Chain B: G.9, T.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.331, A:N.337, A:N.337 NA.9: 2 residues within 4Å: Ligands: G-DT-DC-DG-DG-DA-DC.1, G-DT-DC-DG-DG-DA-DC.1 No protein-ligand interaction detected (PLIP)

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.8: 16 residues within 4Å: Chain A: A.288, E.309, Y.310, K.311, Y.312, R.316, R.332, E.364, F.403, A.439, M.466, K.468, W.485, K.487, K.489 Ligands: G-DT-DC-DG-DG-DA-DC.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.309, A:E.309, A:K.311, A:Y.312, A:R.316, A:R.332, A:K.468 Water bridges: A:R.332, A:R.332 Salt bridges: A:K.311, A:K.487, A:K.489 pi-Stacking: A:F.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumbale, P.P. et al., Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide. To Be Published

Release Date

2025-07-02

Peptides

DNA ligase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase 1

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