SMTL ID : 6ofb.1

Crystal structure of human glutamine-dependent NAD+ synthetase complexed with NaAD+, AMP, pyrophosphate, and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

homo-octamer

Ligands

8 x DND: NICOTINIC ACID ADENINE DINUCLEOTIDE(Non-covalent)

DND.1: 20 residues within 4Å: Chain A: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, D.591, H.649, K.650, F.675, L.676 Chain B: S.348, Q.350, Q.499, L.511, D.536 Ligands: AMP.2 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Q.499, B:Q.499, A:K.529, A:D.531, A:F.675 Salt bridges: A:R.488, A:K.650 pi-Stacking: A:H.649, A:H.649 DND.10: 21 residues within 4Å: Chain A: F.344, Q.350, Q.499, L.511, L.512, D.536 Chain B: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, L.576, D.591, H.649, K.650, F.675 Ligands: AMP.11 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.576 Hydrogen bonds: B:K.529, B:D.531, B:F.675, A:Q.350, A:Q.499, A:Q.499 Salt bridges: B:R.488, B:K.650 pi-Stacking: B:H.649, B:H.649 DND.18: 20 residues within 4Å: Chain C: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, D.591, H.649, K.650, F.675, L.676 Chain D: S.348, Q.350, Q.499, L.511, D.536 Ligands: AMP.19 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.529, C:D.531, C:F.675, D:Q.499, D:Q.499 Salt bridges: C:R.488, C:K.650 pi-Stacking: C:H.649, C:H.649 DND.27: 21 residues within 4Å: Chain C: F.344, Q.350, Q.499, L.511, L.512, D.536 Chain D: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, L.576, D.591, H.649, K.650, F.675 Ligands: AMP.28 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.576 Hydrogen bonds: D:K.529, D:D.531, D:F.675, C:Q.350, C:Q.499, C:Q.499 Salt bridges: D:R.488, D:K.650 pi-Stacking: D:H.649, D:H.649 DND.35: 20 residues within 4Å: Chain E: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, D.591, H.649, K.650, F.675, L.676 Chain F: S.348, Q.350, Q.499, L.511, D.536 Ligands: AMP.36 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.528, E:K.529, E:D.531, E:D.531, E:F.675, F:Q.499, F:Q.499 Salt bridges: E:R.488, E:K.650 pi-Stacking: E:H.649, E:H.649 DND.44: 21 residues within 4Å: Chain E: F.344, Q.350, Q.499, L.511, L.512, D.536 Chain F: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, L.576, D.591, H.649, K.650, F.675 Ligands: AMP.45 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.576 Hydrogen bonds: F:T.528, F:K.529, F:D.531, F:D.531, F:F.675, E:Q.350, E:Q.499, E:Q.499 Salt bridges: F:R.488, F:K.650 pi-Stacking: F:H.649, F:H.649 DND.52: 20 residues within 4Å: Chain G: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, D.591, H.649, K.650, F.675, L.676 Chain H: S.348, Q.350, Q.499, L.511, D.536 Ligands: AMP.53 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:T.528, G:K.529, G:D.531, G:D.531, G:F.675, H:Q.499, H:Q.499 Salt bridges: G:R.488, G:K.650 pi-Stacking: G:H.649, G:H.649 DND.61: 21 residues within 4Å: Chain G: F.344, Q.350, Q.499, L.511, L.512, D.536 Chain H: L.480, Q.483, N.484, R.488, Y.526, L.527, T.528, K.529, D.531, L.576, D.591, H.649, K.650, F.675 Ligands: AMP.62 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: H:L.576 Hydrogen bonds: H:T.528, H:K.529, H:D.531, H:D.531, H:F.675, G:Q.350, G:Q.499, G:Q.499 Salt bridges: H:R.488, H:K.650 pi-Stacking: H:H.649, H:H.649

8 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 12 residues within 4Å: Chain A: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574 Ligands: DND.1, POP.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.419, A:S.516 AMP.11: 13 residues within 4Å: Chain B: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574, L.576 Ligands: DND.10, POP.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.419, B:S.516 AMP.19: 12 residues within 4Å: Chain C: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574 Ligands: DND.18, POP.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.419, C:S.516 AMP.28: 13 residues within 4Å: Chain D: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574, L.576 Ligands: DND.27, POP.29 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.419, D:S.516 AMP.36: 12 residues within 4Å: Chain E: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574 Ligands: DND.35, POP.37 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:M.419, E:S.516 AMP.45: 13 residues within 4Å: Chain F: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574, L.576 Ligands: DND.44, POP.46 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:M.419, F:S.516 AMP.53: 12 residues within 4Å: Chain G: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574 Ligands: DND.52, POP.54 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:M.419, G:S.516 AMP.62: 13 residues within 4Å: Chain H: P.356, L.357, S.358, C.417, Y.418, M.419, R.490, S.516, C.532, A.574, L.576 Ligands: DND.61, POP.63 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:M.419, H:S.516

8 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 9 residues within 4Å: Chain A: S.358, G.360, V.361, D.362, S.363, K.545 Ligands: AMP.2, MG.4, CL.9 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.358, A:S.358, A:G.360, A:V.361, A:D.362, A:D.362, A:S.363 Salt bridges: A:K.545 POP.12: 8 residues within 4Å: Chain B: S.358, G.360, D.362, S.363, K.545 Ligands: AMP.11, MG.13, CL.17 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.358, B:S.358, B:G.360, B:V.361, B:D.362, B:S.363 Salt bridges: B:K.545 POP.20: 9 residues within 4Å: Chain C: S.358, G.360, V.361, D.362, S.363, K.545 Ligands: AMP.19, MG.21, CL.26 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.358, C:S.358, C:G.360, C:V.361, C:D.362, C:D.362, C:S.363 Salt bridges: C:K.545 POP.29: 8 residues within 4Å: Chain D: S.358, G.360, D.362, S.363, K.545 Ligands: AMP.28, MG.30, CL.34 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.358, D:S.358, D:G.360, D:V.361, D:D.362, D:S.363 Salt bridges: D:K.545 POP.37: 9 residues within 4Å: Chain E: S.358, G.360, V.361, D.362, S.363, K.545 Ligands: AMP.36, MG.38, CL.43 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.358, E:S.358, E:G.360, E:V.361, E:D.362, E:D.362, E:S.363 Salt bridges: E:K.545 POP.46: 8 residues within 4Å: Chain F: S.358, G.360, D.362, S.363, K.545 Ligands: AMP.45, MG.47, CL.51 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.358, F:S.358, F:G.360, F:V.361, F:D.362, F:S.363 Salt bridges: F:K.545 POP.54: 9 residues within 4Å: Chain G: S.358, G.360, V.361, D.362, S.363, K.545 Ligands: AMP.53, MG.55, CL.60 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.358, G:S.358, G:G.360, G:V.361, G:D.362, G:D.362, G:S.363 Salt bridges: G:K.545 POP.63: 8 residues within 4Å: Chain H: S.358, G.360, D.362, S.363, K.545 Ligands: AMP.62, MG.64, CL.68 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:S.358, H:S.358, H:G.360, H:V.361, H:D.362, H:S.363 Salt bridges: H:K.545

8 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: G.360, V.361, D.362, K.545 Ligands: POP.3, CL.9 No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain B: G.360, V.361, D.362, K.545 Ligands: POP.12, CL.17 No protein-ligand interaction detected (PLIP) MG.21: 6 residues within 4Å: Chain C: G.360, V.361, D.362, K.545 Ligands: POP.20, CL.26 No protein-ligand interaction detected (PLIP) MG.30: 6 residues within 4Å: Chain D: G.360, V.361, D.362, K.545 Ligands: POP.29, CL.34 No protein-ligand interaction detected (PLIP) MG.38: 6 residues within 4Å: Chain E: G.360, V.361, D.362, K.545 Ligands: POP.37, CL.43 No protein-ligand interaction detected (PLIP) MG.47: 6 residues within 4Å: Chain F: G.360, V.361, D.362, K.545 Ligands: POP.46, CL.51 No protein-ligand interaction detected (PLIP) MG.55: 6 residues within 4Å: Chain G: G.360, V.361, D.362, K.545 Ligands: POP.54, CL.60 No protein-ligand interaction detected (PLIP) MG.64: 6 residues within 4Å: Chain H: G.360, V.361, D.362, K.545 Ligands: POP.63, CL.68 No protein-ligand interaction detected (PLIP)

36 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: P.145, R.146 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.301 Chain F: R.94 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.477 Chain B: H.508, G.509 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: V.361, K.545, R.549, A.572 Ligands: CL.9 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: V.361, K.545, A.572 Ligands: POP.3, MG.4, CL.8 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: G.509 Chain B: R.477 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: S.476 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: V.361, K.545, R.549, A.572 Ligands: CL.17 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: V.361, A.572 Ligands: POP.12, MG.13, CL.16 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain C: P.145, R.146 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain C: R.301 Chain H: R.94 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: R.477 Chain D: H.508, G.509 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain C: V.361, K.545, R.549, A.572 Ligands: CL.26 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain C: V.361, K.545, A.572 Ligands: POP.20, MG.21, CL.25 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain C: G.509 Chain D: R.477 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain D: S.476 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain D: V.361, K.545, R.549, A.572 Ligands: CL.34 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain D: V.361, A.572 Ligands: POP.29, MG.30, CL.33 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain E: P.145, R.146 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain B: R.94 Chain E: R.301 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain E: R.477 Chain F: H.508, G.509 Ligand excluded by PLIP CL.42: 5 residues within 4Å: Chain E: V.361, K.545, R.549, A.572 Ligands: CL.43 Ligand excluded by PLIP CL.43: 6 residues within 4Å: Chain E: V.361, K.545, A.572 Ligands: POP.37, MG.38, CL.42 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain E: G.509 Chain F: R.477 Ligand excluded by PLIP CL.49: 1 residues within 4Å: Chain F: S.476 Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain F: V.361, K.545, R.549, A.572 Ligands: CL.51 Ligand excluded by PLIP CL.51: 5 residues within 4Å: Chain F: V.361, A.572 Ligands: POP.46, MG.47, CL.50 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain G: P.145, R.146 Ligand excluded by PLIP CL.57: 2 residues within 4Å: Chain D: R.94 Chain G: R.301 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain G: R.477 Chain H: H.508, G.509 Ligand excluded by PLIP CL.59: 5 residues within 4Å: Chain G: V.361, K.545, R.549, A.572 Ligands: CL.60 Ligand excluded by PLIP CL.60: 6 residues within 4Å: Chain G: V.361, K.545, A.572 Ligands: POP.54, MG.55, CL.59 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain G: G.509 Chain H: R.477 Ligand excluded by PLIP CL.66: 1 residues within 4Å: Chain H: S.476 Ligand excluded by PLIP CL.67: 5 residues within 4Å: Chain H: V.361, K.545, R.549, A.572 Ligands: CL.68 Ligand excluded by PLIP CL.68: 5 residues within 4Å: Chain H: V.361, A.572 Ligands: POP.63, MG.64, CL.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuenchor, W. et al., Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+synthetases. Nat Commun (2020)

Release Date

2020-01-08

Peptides

Glutamine-dependent NAD(+) synthetase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Glutamine-dependent NAD(+) synthetase