SMTL ID : 1m8k.1 (1 other biounit)

Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Mutant H19A complexed with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: R.11, S.131, G.132, T.133, R.136 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.132, A:T.133, A:T.133 Salt bridges: A:R.11, A:R.136 SO4.3: 6 residues within 4Å: Chain B: R.11, S.131, G.132, T.133, R.136 Ligands: NAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.131, B:G.132, B:T.133, B:T.133 Salt bridges: B:R.11, B:R.136 SO4.5: 6 residues within 4Å: Chain C: R.11, S.131, G.132, T.133, R.136 Ligands: NAD.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.132, C:T.133 Salt bridges: C:R.11, C:R.136 SO4.7: 6 residues within 4Å: Chain D: R.11, S.131, G.132, T.133, R.136 Ligands: NAD.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.132, D:T.133, D:T.133, D:T.133 Salt bridges: D:R.11, D:R.136 SO4.9: 6 residues within 4Å: Chain E: R.11, S.131, G.132, T.133, R.136 Ligands: NAD.10 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.131, E:G.132, E:T.133 Salt bridges: E:R.11, E:R.136 SO4.11: 6 residues within 4Å: Chain F: R.11, S.131, G.132, T.133, R.136 Ligands: NAD.12 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.132, F:T.133, F:T.133 Salt bridges: F:R.11, F:R.136

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

NAD.2: 20 residues within 4Å: Chain A: V.9, G.10, R.11, V.22, G.38, S.39, D.80, I.81, C.83, N.84, W.87, N.105, L.107, V.108, L.111, P.122, L.124, F.125, Y.126 Ligands: SO4.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.107, A:L.111 Hydrogen bonds: A:R.11, A:G.38, A:I.81, A:I.81, A:L.124, A:Y.126, A:Y.126 Salt bridges: A:R.11 pi-Stacking: A:W.87, A:W.87, A:Y.126 NAD.4: 17 residues within 4Å: Chain B: V.9, G.10, R.11, V.22, G.38, S.39, D.80, I.81, N.84, W.87, N.105, L.107, P.122, L.124, F.125, Y.126 Ligands: SO4.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.107 Hydrogen bonds: B:R.11, B:S.39, B:D.80, B:I.81, B:I.81, B:N.84, B:N.105, B:L.124, B:Y.126 Salt bridges: B:R.11 pi-Stacking: B:W.87, B:W.87, B:Y.126 NAD.6: 19 residues within 4Å: Chain C: V.9, G.10, R.11, V.22, G.38, S.39, D.80, I.81, N.84, W.87, N.105, L.107, V.108, L.111, P.122, L.124, F.125, Y.126 Ligands: SO4.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.107, C:L.111 Hydrogen bonds: C:R.11, C:G.38, C:D.80, C:I.81, C:I.81, C:L.124, C:Y.126, C:Y.126 Salt bridges: C:R.11 pi-Stacking: C:W.87, C:W.87, C:Y.126 NAD.8: 20 residues within 4Å: Chain D: V.9, G.10, R.11, V.22, G.38, S.39, D.80, I.81, C.83, N.84, W.87, N.105, L.107, V.108, L.111, P.122, L.124, F.125, Y.126 Ligands: SO4.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.107, D:L.111 Hydrogen bonds: D:R.11, D:G.38, D:D.80, D:I.81, D:I.81, D:L.124, D:Y.126, D:Y.126 Salt bridges: D:R.11 pi-Stacking: D:W.87, D:W.87, D:Y.126 NAD.10: 17 residues within 4Å: Chain E: V.9, G.10, R.11, V.22, G.38, S.39, D.80, I.81, N.84, W.87, N.105, L.107, P.122, L.124, F.125, Y.126 Ligands: SO4.9 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.107 Hydrogen bonds: E:R.11, E:S.39, E:I.81, E:I.81, E:N.84, E:N.105, E:L.124, E:Y.126 Salt bridges: E:R.11 pi-Stacking: E:W.87, E:W.87, E:Y.126 NAD.12: 19 residues within 4Å: Chain F: V.9, G.10, R.11, V.22, G.38, S.39, D.80, I.81, N.84, W.87, N.105, L.107, V.108, L.111, P.122, L.124, F.125, Y.126 Ligands: SO4.11 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.107, F:L.111 Hydrogen bonds: F:R.11, F:G.38, F:I.81, F:I.81, F:L.124, F:Y.126, F:Y.126 Salt bridges: F:R.11 pi-Stacking: F:W.87, F:W.87, F:Y.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saridakis, V. et al., Mutational, Structural, and Kinetic Studies of the ATP-binding Site of Methanobacterium thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase. J.Biol.Chem. (2003)

Release Date

2003-07-15

Peptides

Nicotinamide-nucleotide Adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Nicotinamide-nucleotide Adenylyltransferase

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