SMTL ID : 1tae.5 (5 other biounits)

Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: Y.30, G.123, L.124, A.125, R.141, R.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.125 Water bridges: A:R.141, A:G.142 Salt bridges: A:R.141, A:R.202 SO4.2: 4 residues within 4Å: Chain A: A.80, P.81, R.129, R.137 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.78, A:K.79, A:R.137, A:R.137 Salt bridges: A:R.129, A:R.137 SO4.3: 8 residues within 4Å: Chain A: H.82, D.83, I.84, S.127, R.129, R.137, E.171, R.173 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.83, A:S.127, A:E.171 Water bridges: A:R.129, A:R.137 Salt bridges: A:H.82, A:R.129, A:R.137, A:R.173 SO4.4: 5 residues within 4Å: Chain A: Y.177, P.179, N.223, R.253, P.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.177, A:N.223 Salt bridges: A:R.253 SO4.5: 2 residues within 4Å: Chain A: T.304, R.309 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.309 SO4.6: 6 residues within 4Å: Chain A: R.14, Q.21 Chain B: W.268, E.272, H.275, Y.314 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.21, B:Y.314 Salt bridges: A:R.14, B:H.275 SO4.7: 4 residues within 4Å: Chain A: V.160, P.161, M.162, R.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.162, A:R.163 SO4.10: 6 residues within 4Å: Chain B: Y.30, G.123, L.124, A.125, R.141, R.202 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.125 Water bridges: B:G.142, B:G.142 Salt bridges: B:R.141, B:R.202 SO4.11: 5 residues within 4Å: Chain B: K.79, A.80, P.81, R.129, R.137 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.129, B:R.137 SO4.12: 4 residues within 4Å: Chain B: R.190, F.198, Q.211, R.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.211 Salt bridges: B:R.190, B:R.220 SO4.13: 9 residues within 4Å: Chain B: P.81, H.82, D.83, I.84, S.127, R.129, R.137, E.171, R.173 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.83, B:S.127 Water bridges: B:S.127, B:R.137 Salt bridges: B:H.82, B:R.129, B:R.137, B:R.173 SO4.14: 7 residues within 4Å: Chain B: S.26, Y.30, Y.42, Y.46, R.68, K.306 Ligands: NAD.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.26, B:Y.30, B:Y.42 Water bridges: B:S.88, B:R.141 Salt bridges: B:K.306 SO4.15: 4 residues within 4Å: Chain A: W.268, H.275, Y.314 Chain B: R.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.14, A:H.275 Hydrogen bonds: A:Y.314

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

NA.8: 3 residues within 4Å: Chain A: E.38, D.39, N.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.38, A:D.39, A:N.200 Water bridges: A:Y.40

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.9: 24 residues within 4Å: Chain A: Y.25, S.26, Y.29, Y.30, P.35, V.37, D.39, Y.42, D.43, Y.87, S.88, L.89, D.91, E.118, L.119, K.120, I.121, A.125, R.141, E.175, Y.227, V.289, K.291, K.315 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.29, A:Y.30, A:Y.42 Hydrogen bonds: A:Y.30, A:D.39, A:D.39, A:D.43, A:Y.87, A:E.118, A:I.121, A:K.291, A:K.315 Water bridges: A:L.119, A:K.120, A:A.125, A:K.306 Salt bridges: A:K.120, A:R.141, A:K.315 pi-Stacking: A:Y.29, A:Y.42, A:Y.227 NAD.16: 26 residues within 4Å: Chain B: Y.25, S.26, Y.29, Y.30, P.35, V.37, E.38, D.39, Y.42, D.43, Y.87, S.88, L.89, D.91, E.118, L.119, K.120, I.121, A.125, R.141, E.175, Y.227, V.289, K.291, K.315 Ligands: SO4.14 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:Y.29, B:Y.30, B:Y.42 Hydrogen bonds: B:Y.30, B:V.37, B:D.43, B:Y.87, B:L.89, B:L.119, B:K.120, B:I.121, B:R.141, B:Y.227, B:K.291, B:K.315, B:K.315 Water bridges: B:L.119, B:R.141, B:G.174, B:Y.227, B:K.306 Salt bridges: B:K.120, B:K.120, B:R.141, B:K.315 pi-Stacking: B:Y.29, B:Y.42, B:Y.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gajiwala, K.S. et al., Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. STRUCTURE (2004)

Release Date

2004-11-23

Peptides

DNA ligase, NAD-dependent: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

DNA ligase, NAD-dependent

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