SMTL ID : 6lw8.1

Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: V.241, E.242, G.243, F.244, R.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.243 GOL.9: 5 residues within 4Å: Chain B: V.241, E.242, G.243, F.244, R.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.243

2 x EWO: (4R)-4-(4-fluorophenyl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine(Non-covalent)

EWO.2: 9 residues within 4Å: Chain A: H.27, Q.28, Y.31, Y.32, P.37, I.39, S.40, D.41, F.44 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.31, A:F.44, A:F.44 Hydrogen bonds: A:Y.32 EWO.10: 9 residues within 4Å: Chain B: H.27, Q.28, Y.31, Y.32, P.37, I.39, S.40, D.41, F.44 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.31, B:F.44, B:F.44 Hydrogen bonds: B:Y.32

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

SO4.3: 5 residues within 4Å: Chain A: E.202, K.204, V.225, R.228, R.229 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.229, A:R.229 Salt bridges: A:K.204, A:R.228, A:R.229 SO4.4: 5 residues within 4Å: Chain A: L.199, K.204, F.207, Q.220, R.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.220 Salt bridges: A:K.204, A:R.229 SO4.5: 5 residues within 4Å: Chain A: G.126, V.127, A.128, R.144, R.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.128, A:R.211 Water bridges: A:A.128 Salt bridges: A:R.144 SO4.6: 6 residues within 4Å: Chain A: R.30, R.34, V.163, P.164, E.165 Chain B: P.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.165 Salt bridges: A:R.30, A:R.34 SO4.7: 6 residues within 4Å: Chain A: A.98, L.101, R.277, I.280, D.281, Y.323 No protein-ligand interaction detected (PLIP) SO4.8: 3 residues within 4Å: Chain A: N.94, K.123, K.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.94 Salt bridges: A:K.123, A:K.324 SO4.11: 5 residues within 4Å: Chain B: E.202, K.204, V.225, R.228, R.229 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.229, B:R.229 Salt bridges: B:K.204, B:R.228, B:R.229 SO4.12: 5 residues within 4Å: Chain B: L.199, K.204, F.207, Q.220, R.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.220 Salt bridges: B:K.204, B:R.229 SO4.13: 5 residues within 4Å: Chain B: G.126, V.127, A.128, R.144, R.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.128, B:R.211 Water bridges: B:A.128 Salt bridges: B:R.144 SO4.14: 6 residues within 4Å: Chain A: P.11 Chain B: R.30, R.34, V.163, P.164, E.165 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.165 Salt bridges: B:R.30, B:R.34 SO4.15: 6 residues within 4Å: Chain B: A.98, L.101, R.277, I.280, D.281, Y.323 No protein-ligand interaction detected (PLIP) SO4.16: 3 residues within 4Å: Chain B: N.94, K.123, K.324 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.94 Salt bridges: B:K.123, B:K.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shukla, A. et al., Structure based identification of first-in-class fragment inhibitors that target the NMN pocket of M. tuberculosis NAD + -dependent DNA ligase A. J.Struct.Biol. (2021)

Release Date

2021-02-10

Peptides

DNA ligase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA ligase A

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