SMTL ID : 1m8j.1

Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Mutant R136A complexed with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: H.16, H.19, Y.130, S.131, G.132 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.132 Water bridges: A:R.11, A:M.12 Salt bridges: A:H.16, A:H.19 SO4.3: 6 residues within 4Å: Chain B: H.16, H.19, Y.130, S.131, G.132 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.132 Water bridges: B:R.11, B:M.12 Salt bridges: B:H.16, B:H.19 SO4.5: 6 residues within 4Å: Chain C: H.16, H.19, Y.130, S.131, G.132 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.132 Water bridges: C:R.11, C:M.12 Salt bridges: C:H.16, C:H.19 SO4.7: 6 residues within 4Å: Chain D: H.16, H.19, Y.130, S.131, G.132 Ligands: NAD.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.132 Water bridges: D:R.11, D:M.12 Salt bridges: D:H.16, D:H.19 SO4.9: 6 residues within 4Å: Chain E: H.16, H.19, Y.130, S.131, G.132 Ligands: NAD.10 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.132 Water bridges: E:R.11, E:M.12 Salt bridges: E:H.16, E:H.19 SO4.11: 6 residues within 4Å: Chain F: H.16, H.19, Y.130, S.131, G.132 Ligands: NAD.12 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.132 Water bridges: F:R.11, F:M.12 Salt bridges: F:H.16, F:H.19

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

NAD.2: 26 residues within 4Å: Chain A: V.9, G.10, R.11, M.12, H.16, G.18, H.19, G.38, S.39, D.80, I.81, N.84, W.87, S.103, G.104, N.105, L.107, V.108, L.111, P.123, L.124, F.125, Y.126, R.127, Y.130 Ligands: SO4.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.87, A:W.87, A:W.87, A:L.107, A:L.111 Hydrogen bonds: A:R.11, A:M.12, A:G.38, A:S.39, A:D.80, A:I.81, A:S.103, A:G.104, A:N.105, A:F.125, A:Y.130 Water bridges: A:R.11, A:R.11, A:S.39 Salt bridges: A:R.11, A:R.11, A:H.19 NAD.4: 26 residues within 4Å: Chain B: V.9, G.10, R.11, M.12, H.16, G.18, H.19, G.38, S.39, D.80, I.81, N.84, W.87, S.103, G.104, N.105, L.107, V.108, L.111, P.123, L.124, F.125, Y.126, R.127, Y.130 Ligands: SO4.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.87, B:W.87, B:W.87, B:L.107, B:L.111 Hydrogen bonds: B:R.11, B:M.12, B:G.38, B:S.39, B:D.80, B:I.81, B:S.103, B:G.104, B:N.105, B:F.125, B:Y.130 Water bridges: B:R.11, B:R.11, B:S.39 Salt bridges: B:R.11, B:R.11, B:H.19 NAD.6: 26 residues within 4Å: Chain C: V.9, G.10, R.11, M.12, H.16, G.18, H.19, G.38, S.39, D.80, I.81, N.84, W.87, S.103, G.104, N.105, L.107, V.108, L.111, P.123, L.124, F.125, Y.126, R.127, Y.130 Ligands: SO4.5 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:W.87, C:W.87, C:W.87, C:L.107, C:L.111 Hydrogen bonds: C:R.11, C:M.12, C:G.38, C:S.39, C:D.80, C:I.81, C:S.103, C:G.104, C:N.105, C:F.125, C:Y.130 Water bridges: C:R.11, C:R.11, C:S.39 Salt bridges: C:R.11, C:R.11, C:H.19 NAD.8: 26 residues within 4Å: Chain D: V.9, G.10, R.11, M.12, H.16, G.18, H.19, G.38, S.39, D.80, I.81, N.84, W.87, S.103, G.104, N.105, L.107, V.108, L.111, P.123, L.124, F.125, Y.126, R.127, Y.130 Ligands: SO4.7 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:W.87, D:W.87, D:W.87, D:L.107, D:L.111 Hydrogen bonds: D:R.11, D:M.12, D:G.38, D:S.39, D:D.80, D:D.80, D:I.81, D:S.103, D:G.104, D:N.105, D:F.125, D:Y.130 Water bridges: D:R.11, D:R.11, D:S.39 Salt bridges: D:R.11, D:R.11, D:H.19 NAD.10: 26 residues within 4Å: Chain E: V.9, G.10, R.11, M.12, H.16, G.18, H.19, G.38, S.39, D.80, I.81, N.84, W.87, S.103, G.104, N.105, L.107, V.108, L.111, P.123, L.124, F.125, Y.126, R.127, Y.130 Ligands: SO4.9 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:W.87, E:W.87, E:W.87, E:L.107, E:L.111 Hydrogen bonds: E:R.11, E:M.12, E:G.38, E:S.39, E:D.80, E:D.80, E:I.81, E:S.103, E:G.104, E:N.105, E:F.125, E:Y.130 Water bridges: E:R.11, E:R.11, E:S.39 Salt bridges: E:R.11, E:R.11, E:H.19 NAD.12: 26 residues within 4Å: Chain F: V.9, G.10, R.11, M.12, H.16, G.18, H.19, G.38, S.39, D.80, I.81, N.84, W.87, S.103, G.104, N.105, L.107, V.108, L.111, P.123, L.124, F.125, Y.126, R.127, Y.130 Ligands: SO4.11 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:W.87, F:W.87, F:W.87, F:L.107, F:L.111 Hydrogen bonds: F:R.11, F:M.12, F:G.38, F:S.39, F:D.80, F:D.80, F:I.81, F:S.103, F:G.104, F:N.105, F:F.125, F:Y.130 Water bridges: F:R.11, F:R.11, F:S.39 Salt bridges: F:R.11, F:R.11, F:H.19

Links

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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
A

C
A

D
A

E
A

F
A

Nicotinamide-nucleotide Adenylyltransferase