SMTL ID : 5db4.3 (2 other biounits)

Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: M.16, G.17, G.18, T.19, F.20, H.24, G.26, H.27, R.57, T.114, G.115, D.117, A.118, S.141, R.142, L.170, I.172, S.173, S.174, T.175, R.178 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:T.19, A:F.20, A:R.57, A:G.115, A:D.117, A:A.118, A:R.142, A:I.172, A:S.174, A:T.175, A:T.175, A:T.175 Water bridges: A:R.142, A:R.142, A:R.142, A:L.170, A:I.172, A:R.178, A:R.178 Salt bridges: A:H.24, A:H.27, A:H.27, A:R.142, A:R.178 ATP.3: 22 residues within 4Å: Chain B: M.16, G.17, G.18, T.19, F.20, H.24, G.26, H.27, T.114, G.115, D.117, A.118, V.140, S.141, R.142, L.170, I.172, S.173, S.174, T.175, R.178 Ligands: MG.4 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:T.19, B:T.19, B:F.20, B:T.114, B:G.115, B:D.117, B:R.142, B:I.172, B:I.172, B:S.174, B:T.175, B:T.175, B:T.175 Water bridges: B:R.142, B:R.142, B:L.170, B:S.174, B:S.174, B:T.175 Salt bridges: B:H.24, B:H.27, B:H.27, B:R.142, B:R.178 pi-Cation interactions: B:R.142 ATP.5: 22 residues within 4Å: Chain C: M.16, G.17, G.18, T.19, F.20, H.24, G.26, H.27, R.57, T.114, G.115, D.117, A.118, S.141, R.142, L.170, I.172, S.173, S.174, T.175, R.178 Ligands: MG.6 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:T.19, C:F.20, C:R.57, C:G.115, C:D.117, C:A.118, C:R.142, C:I.172, C:S.174, C:T.175, C:T.175, C:T.175 Water bridges: C:R.142, C:R.142, C:R.142, C:L.170, C:I.172, C:R.178, C:R.178 Salt bridges: C:H.24, C:H.27, C:H.27, C:R.142, C:R.178 ATP.7: 22 residues within 4Å: Chain D: M.16, G.17, G.18, T.19, F.20, H.24, G.26, H.27, T.114, G.115, D.117, A.118, V.140, S.141, R.142, L.170, I.172, S.173, S.174, T.175, R.178 Ligands: MG.8 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:T.19, D:T.19, D:F.20, D:T.114, D:G.115, D:D.117, D:R.142, D:I.172, D:I.172, D:S.174, D:T.175, D:T.175, D:T.175 Water bridges: D:R.142, D:R.142, D:L.170, D:S.174, D:S.174, D:T.175 Salt bridges: D:H.24, D:H.27, D:H.27, D:R.142, D:R.178 pi-Cation interactions: D:R.142

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

MG.2: 2 residues within 4Å: Chain A: R.142 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: R.142 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reed, R.W. et al., Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41. to be published

Release Date

2016-08-24

Peptides

Nicotinate-nucleotide adenylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Nicotinate-nucleotide adenylyltransferase

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