SMTL ID : 1ej2.2 (1 other biounit)

Crystal structure of methanobacterium thermoautotrophicum nicotinamide mononucleotide adenylyltransferase with bound NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: R.11, R.47, S.131, G.132, T.133, R.136 Ligands: NA.2, NAD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.132, A:T.133, A:T.133 Water bridges: A:T.133, A:R.136 Salt bridges: A:R.11, A:R.47, A:R.136 SO4.4: 8 residues within 4Å: Chain B: R.11, R.47, S.131, G.132, T.133, R.136 Ligands: NA.5, NAD.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.132, B:T.133, B:T.133 Water bridges: B:T.133, B:R.136 Salt bridges: B:R.11, B:R.47, B:R.136 SO4.7: 8 residues within 4Å: Chain C: R.11, R.47, S.131, G.132, T.133, R.136 Ligands: NA.8, NAD.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.132, C:T.133, C:T.133 Water bridges: C:T.133, C:R.136 Salt bridges: C:R.11, C:R.47, C:R.136 SO4.10: 8 residues within 4Å: Chain D: R.11, R.47, S.131, G.132, T.133, R.136 Ligands: NA.11, NAD.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.132, D:T.133 Water bridges: D:T.133, D:T.133, D:R.136 Salt bridges: D:R.11, D:R.47, D:R.136 SO4.13: 8 residues within 4Å: Chain E: R.11, R.47, S.131, G.132, T.133, R.136 Ligands: NA.14, NAD.15 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.132, E:T.133 Water bridges: E:T.133, E:T.133, E:R.136 Salt bridges: E:R.11, E:R.47, E:R.136 SO4.16: 8 residues within 4Å: Chain F: R.11, R.47, S.131, G.132, T.133, R.136 Ligands: NA.17, NAD.18 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.132, F:T.133 Water bridges: F:T.133, F:T.133, F:R.136 Salt bridges: F:R.11, F:R.47, F:R.136

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

NA.2: 5 residues within 4Å: Chain A: R.11, M.12, Q.13 Ligands: SO4.1, NAD.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.13 NA.5: 5 residues within 4Å: Chain B: R.11, M.12, Q.13 Ligands: SO4.4, NAD.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.13 NA.8: 5 residues within 4Å: Chain C: R.11, M.12, Q.13 Ligands: SO4.7, NAD.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.13 NA.11: 5 residues within 4Å: Chain D: R.11, M.12, Q.13 Ligands: SO4.10, NAD.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.13 NA.14: 5 residues within 4Å: Chain E: R.11, M.12, Q.13 Ligands: SO4.13, NAD.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.13 NA.17: 5 residues within 4Å: Chain F: R.11, M.12, Q.13 Ligands: SO4.16, NAD.18 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.13

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

NAD.3: 27 residues within 4Å: Chain A: L.8, V.9, G.10, R.11, M.12, H.16, G.18, H.19, V.22, 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.130 Ligands: SO4.1, NA.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.87, A:W.87, A:L.107, A:V.108, A:L.111 Hydrogen bonds: A:R.11, A:R.11, A:M.12, A:G.38, A:I.81, A:I.81, A:G.104, A:N.105, A:N.105, A:F.125, A:F.125 Water bridges: A:V.9, A:S.39, A:D.80, A:N.84, A:S.103 Salt bridges: A:H.19 NAD.6: 27 residues within 4Å: Chain B: L.8, V.9, G.10, R.11, M.12, H.16, G.18, H.19, V.22, 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.130 Ligands: SO4.4, NA.5 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.87, B:W.87, B:L.107, B:V.108, B:L.111 Hydrogen bonds: B:R.11, B:R.11, B:M.12, B:G.38, B:I.81, B:I.81, B:G.104, B:N.105, B:N.105, B:F.125, B:F.125 Water bridges: B:V.9, B:S.39, B:D.80, B:N.84, B:S.103 Salt bridges: B:H.19 NAD.9: 27 residues within 4Å: Chain C: L.8, V.9, G.10, R.11, M.12, H.16, G.18, H.19, V.22, 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.130 Ligands: SO4.7, NA.8 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:W.87, C:W.87, C:L.107, C:V.108, C:L.111 Hydrogen bonds: C:R.11, C:R.11, C:M.12, C:G.38, C:I.81, C:I.81, C:G.104, C:N.105, C:N.105, C:F.125, C:F.125 Water bridges: C:V.9, C:S.39, C:D.80, C:N.84, C:S.103 Salt bridges: C:H.19 NAD.12: 27 residues within 4Å: Chain D: L.8, V.9, G.10, R.11, M.12, H.16, G.18, H.19, V.22, 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.130 Ligands: SO4.10, NA.11 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:W.87, D:W.87, D:L.107, D:V.108, D:L.111 Hydrogen bonds: D:R.11, D:R.11, D:M.12, D:G.38, D:D.80, D:I.81, D:I.81, D:G.104, D:N.105, D:N.105, D:F.125, D:F.125 Water bridges: D:V.9, D:S.39, D:D.80, D:N.84, D:S.103 Salt bridges: D:H.19 NAD.15: 27 residues within 4Å: Chain E: L.8, V.9, G.10, R.11, M.12, H.16, G.18, H.19, V.22, 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.130 Ligands: SO4.13, NA.14 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:W.87, E:W.87, E:L.107, E:V.108, E:L.111 Hydrogen bonds: E:R.11, E:R.11, E:M.12, E:G.38, E:D.80, E:I.81, E:I.81, E:G.104, E:N.105, E:N.105, E:F.125, E:F.125 Water bridges: E:V.9, E:S.39, E:D.80, E:N.84, E:S.103 Salt bridges: E:H.19 NAD.18: 27 residues within 4Å: Chain F: L.8, V.9, G.10, R.11, M.12, H.16, G.18, H.19, V.22, 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.130 Ligands: SO4.16, NA.17 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:W.87, F:W.87, F:L.107, F:V.108, F:L.111 Hydrogen bonds: F:R.11, F:R.11, F:M.12, F:G.38, F:D.80, F:I.81, F:I.81, F:G.104, F:N.105, F:N.105, F:F.125, F:F.125 Water bridges: F:V.9, F:S.39, F:D.80, F:N.84, F:S.103 Salt bridges: F:H.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saridakis, V. et al., Insights into ligand binding and catalysis of a central step in NAD+ synthesis: structures of Methanobacterium thermoautotrophicum NMN adenylyltransferase complexes. J.Biol.Chem. (2001)

Release Date

2001-03-14

Peptides

NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE

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