SMTL ID : 1nus.1

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE COMPLEXED WITH ATP ANALOG AND NMN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.95, R.98, H.152 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.95 Salt bridges: A:K.95, A:R.98, A:K.149, A:H.152 SO4.4: 4 residues within 4Å: Chain B: K.95, R.98, K.149, H.152 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:K.95, B:R.98, B:K.149, B:H.152 SO4.7: 3 residues within 4Å: Chain C: K.95, R.98, H.152 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.95 Salt bridges: C:K.95, C:R.98, C:K.149, C:H.152 SO4.10: 4 residues within 4Å: Chain D: K.95, R.98, K.149, H.152 4 PLIP interactions: 4 interactions with chain D Salt bridges: D:K.95, D:R.98, D:K.149, D:H.152

4 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.2: 10 residues within 4Å: Chain A: C.12, G.13, V.49, Y.53, K.55, W.90, E.92, T.93, L.147, W.148 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:Y.53, A:W.90, A:T.93, A:L.147 Water bridges: A:G.13, A:G.13, A:S.14, A:K.55, A:K.149 Salt bridges: A:K.55 pi-Stacking: A:W.148 NMN.5: 11 residues within 4Å: Chain B: C.12, G.13, V.49, Y.53, K.55, W.90, E.92, T.93, L.147, W.148 Ligands: APC.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.53, B:T.93, B:T.93, B:L.147 Water bridges: B:G.13, B:K.149 Salt bridges: B:K.55 pi-Stacking: B:W.148 NMN.8: 10 residues within 4Å: Chain C: C.12, G.13, V.49, Y.53, K.55, W.90, E.92, T.93, L.147, W.148 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.147 Hydrogen bonds: C:W.90, C:T.93, C:T.93, C:L.147 Water bridges: C:G.13, C:G.13, C:S.14, C:K.55, C:K.149, C:H.152, C:H.152 Salt bridges: C:K.55 pi-Stacking: C:W.148 NMN.11: 11 residues within 4Å: Chain D: C.12, G.13, V.49, Y.53, K.55, W.90, E.92, T.93, L.147, W.148 Ligands: APC.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.93, D:T.93, D:L.147 Water bridges: D:G.13, D:K.149, D:H.152, D:H.152 Salt bridges: D:K.55 pi-Stacking: D:W.148

4 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.3: 19 residues within 4Å: Chain A: C.12, G.13, S.14, F.15, M.21, H.22, M.25, K.56, C.134, G.135, D.137, V.138, R.167, N.198, I.200, A.202, T.203, R.206 Chain B: K.140 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.14, A:F.15, A:G.135, A:D.137, A:N.198, A:A.202, A:T.203, A:T.203, A:T.203, A:T.203, B:K.140 Water bridges: A:S.14, A:R.206, A:R.206 Salt bridges: A:K.55, A:K.56, A:R.206, B:K.140 pi-Cation interactions: A:R.167, A:R.167 APC.6: 21 residues within 4Å: Chain A: K.140 Chain B: C.12, G.13, S.14, F.15, M.21, H.22, M.25, K.56, C.134, G.135, D.137, V.138, R.167, N.198, E.199, I.200, A.202, T.203, R.206 Ligands: NMN.5 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.14, B:S.14, B:F.15, B:G.135, B:D.137, B:R.167, B:N.198, B:I.200, B:A.202, B:T.203, B:T.203, B:T.203, B:T.203, A:K.140 Salt bridges: B:K.55, B:K.56, B:R.206, A:K.140 pi-Cation interactions: B:R.167, B:R.167 APC.9: 19 residues within 4Å: Chain C: C.12, G.13, S.14, F.15, M.21, H.22, M.25, K.56, C.134, G.135, D.137, V.138, R.167, N.198, I.200, A.202, T.203, R.206 Chain D: K.140 19 PLIP interactions: 2 interactions with chain D, 17 interactions with chain C Hydrogen bonds: D:K.140, C:S.14, C:F.15, C:G.135, C:D.137, C:N.198, C:A.202, C:T.203, C:T.203, C:T.203 Salt bridges: D:K.140, C:K.55, C:K.56, C:R.206 Water bridges: C:S.14, C:R.206, C:R.206 pi-Cation interactions: C:R.167, C:R.167 APC.12: 21 residues within 4Å: Chain C: K.140 Chain D: C.12, G.13, S.14, F.15, M.21, H.22, M.25, K.56, C.134, G.135, D.137, V.138, R.167, N.198, E.199, I.200, A.202, T.203, R.206 Ligands: NMN.11 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.14, D:S.14, D:F.15, D:G.135, D:D.137, D:R.167, D:N.198, D:I.200, D:A.202, D:T.203, D:T.203, D:T.203, C:K.140 Salt bridges: D:K.55, D:K.56, D:R.206, C:K.140 pi-Cation interactions: D:R.167, D:R.167

Links

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Citation

ZHANG, X. et al., STRUCTURAL CHARACTERIZATION OF A HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE AND IMPLICATION IN HUMAN NAD BIOSYNTHESIS. J.Biol.Chem. (2003)

Release Date

2003-06-03

Peptides

FKSG76: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

FKSG76

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