SMTL ID : 1kqn.1

Crystal structure of NMN/NaMN adenylyltransferase complexed with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: C.14, G.15, S.16, F.17, M.23, H.24, L.27, V.51, Y.55, K.57, E.86, W.92, E.94, T.95, C.155, G.156, D.158, L.159, L.168, W.169, V.186, E.215, N.219, P.269 Ligands: XE.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.92, A:L.168, A:P.269 Hydrogen bonds: A:C.14, A:S.16, A:F.17, A:W.92, A:T.95, A:T.95, A:T.95, A:G.156, A:L.159, A:N.219 Water bridges: A:G.15, A:H.24, A:Y.55, A:K.57, A:K.57, A:K.57, A:L.96, A:A.157, A:D.158, A:K.170, A:S.223 Salt bridges: A:H.24, A:K.57, A:K.57 pi-Stacking: A:W.169 NAD.5: 24 residues within 4Å: Chain B: C.14, G.15, S.16, F.17, M.23, H.24, L.27, V.51, Y.55, K.57, W.92, E.94, T.95, C.155, G.156, D.158, L.159, L.168, W.169, V.186, E.215, N.219, D.220, P.269 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:W.92, B:L.168, B:P.269 Hydrogen bonds: B:C.14, B:S.16, B:F.17, B:W.92, B:T.95, B:T.95, B:G.156, B:L.159, B:D.220 Water bridges: B:C.14, B:G.15, B:L.96, B:A.157, B:D.158, B:K.170, B:D.173, B:R.188, B:S.223, B:N.273 Salt bridges: B:H.24, B:K.57, B:K.57 pi-Stacking: B:W.169 NAD.10: 23 residues within 4Å: Chain C: C.14, G.15, S.16, F.17, M.23, H.24, L.27, V.51, Y.55, K.57, W.92, E.94, T.95, C.155, G.156, D.158, L.159, L.168, W.169, V.186, E.215, N.219, P.269 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:W.92, C:L.168, C:P.269 Hydrogen bonds: C:C.14, C:S.16, C:F.17, C:W.92, C:T.95, C:T.95, C:T.95, C:G.156, C:L.159, C:N.219 Water bridges: C:G.15, C:H.24, C:K.57, C:K.57, C:L.96, C:K.170, C:D.173, C:S.223 Salt bridges: C:H.24, C:K.57, C:K.57 pi-Stacking: C:W.169 NAD.14: 24 residues within 4Å: Chain D: C.14, G.15, S.16, F.17, M.23, H.24, L.27, V.51, Y.55, K.57, W.92, E.94, T.95, C.155, G.156, L.159, L.168, W.169, V.186, E.215, N.219, P.269 Ligands: XE.15, XE.16 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:W.92, D:L.168, D:P.269 Hydrogen bonds: D:C.14, D:C.14, D:S.16, D:F.17, D:W.92, D:T.95, D:T.95, D:G.156, D:L.159, D:N.219 Water bridges: D:G.15, D:N.18, D:H.24, D:L.96, D:A.157, D:D.158, D:K.170, D:D.173, D:R.188, D:S.223, D:N.273 Salt bridges: D:H.24, D:K.57, D:K.57 pi-Stacking: D:W.169 NAD.17: 21 residues within 4Å: Chain E: C.14, G.15, S.16, F.17, M.23, H.24, L.27, V.51, Y.55, K.57, W.92, E.94, T.95, C.155, G.156, D.158, L.159, L.168, W.169, V.186, P.269 28 PLIP interactions: 28 interactions with chain E Hydrophobic interactions: E:W.92, E:L.168, E:P.269 Hydrogen bonds: E:C.14, E:S.16, E:F.17, E:W.92, E:T.95, E:T.95, E:T.95, E:G.156, E:D.158, E:L.159 Water bridges: E:G.15, E:N.18, E:H.24, E:L.96, E:D.158, E:D.173, E:D.173, E:R.188, E:N.219, E:S.223, E:N.273 Salt bridges: E:H.24, E:K.57, E:K.57 pi-Stacking: E:W.169 NAD.20: 24 residues within 4Å: Chain F: C.14, G.15, S.16, F.17, M.23, H.24, L.27, V.51, Y.55, K.57, W.92, E.94, T.95, C.155, G.156, D.158, L.159, L.168, W.169, V.186, E.215, N.219, P.269 Ligands: XE.21 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:W.92, F:L.168, F:P.269 Hydrogen bonds: F:C.14, F:S.16, F:F.17, F:H.24, F:W.92, F:T.95, F:T.95, F:G.156, F:L.159, F:N.219 Water bridges: F:G.15, F:H.24, F:D.158, F:S.223, F:S.223 Salt bridges: F:H.24, F:K.57, F:K.57 pi-Stacking: F:W.169

15 x XE: XENON(Non-covalent)(Non-functional Binders)

XE.2: 2 residues within 4Å: Chain A: S.87, L.88 No protein-ligand interaction detected (PLIP) XE.3: 6 residues within 4Å: Chain A: M.23, R.26, L.27, E.215, N.219 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) XE.4: 2 residues within 4Å: Chain A: F.196, S.200 No protein-ligand interaction detected (PLIP) XE.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) XE.7: 1 residues within 4Å: Chain B: S.200 No protein-ligand interaction detected (PLIP) XE.8: 3 residues within 4Å: Chain B: M.23, L.27, E.215 No protein-ligand interaction detected (PLIP) XE.9: 3 residues within 4Å: Chain B: A.13, H.24, L.27 No protein-ligand interaction detected (PLIP) XE.11: 5 residues within 4Å: Chain C: M.23, R.26, L.27, L.30, E.215 No protein-ligand interaction detected (PLIP) XE.12: 1 residues within 4Å: Chain C: S.200 No protein-ligand interaction detected (PLIP) XE.13: 3 residues within 4Å: Chain C: S.87, L.88, Q.89 No protein-ligand interaction detected (PLIP) XE.15: 4 residues within 4Å: Chain D: A.13, H.24, L.27 Ligands: NAD.14 No protein-ligand interaction detected (PLIP) XE.16: 4 residues within 4Å: Chain D: M.23, L.27, E.215 Ligands: NAD.14 No protein-ligand interaction detected (PLIP) XE.18: 2 residues within 4Å: Chain E: H.24, L.27 No protein-ligand interaction detected (PLIP) XE.19: 3 residues within 4Å: Chain E: M.23, L.27, E.215 No protein-ligand interaction detected (PLIP) XE.21: 5 residues within 4Å: Chain F: M.23, L.27, E.215, N.219 Ligands: NAD.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structure of Human Nicotinamide/Nicotonic Acid Mononucleotide Adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. J.Biol.Chem. (2003)

Release Date

2003-01-07

Peptides

NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE

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