SMTL ID : 8x7f.1

CryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: F.7, G.8, K.9, F.10, H.14, G.16, H.17, L.20, E.81, E.85, P.86, Y.87, G.90, W.91, W.94, T.114, S.115, E.116, R.138, M.141 Ligands: PO4.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.87, A:W.91, A:W.94 Hydrogen bonds: A:F.7, A:K.9, A:F.10, A:E.81, A:E.81, A:Y.87, A:G.90, A:T.114, A:S.115, A:S.115, A:E.116, A:R.138, A:R.138, A:M.141 Salt bridges: A:H.17 pi-Cation interactions: A:R.138, A:R.138 NAD.3: 21 residues within 4Å: Chain B: F.7, G.8, K.9, F.10, H.14, G.16, H.17, L.20, E.81, E.85, P.86, Y.87, G.90, W.91, W.94, T.114, S.115, E.116, R.138, M.141 Ligands: PO4.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.87, B:W.91, B:W.94 Hydrogen bonds: B:K.9, B:F.10, B:E.81, B:E.85, B:G.90, B:T.114, B:S.115, B:S.115, B:E.116, B:R.138, B:R.138, B:I.143 Salt bridges: B:H.17 pi-Cation interactions: B:R.138, B:R.138 NAD.5: 18 residues within 4Å: Chain C: F.7, G.8, K.9, F.10, H.14, G.16, H.17, L.20, E.81, Y.87, G.90, W.91, W.94, T.114, S.115, E.116, R.138, M.141 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.87 Hydrogen bonds: C:K.9, C:F.10, C:G.36, C:E.81, C:G.90, C:S.115, C:S.115, C:E.116, C:E.116, C:R.138, C:R.138, C:I.143 Salt bridges: C:K.9, C:H.17 pi-Cation interactions: C:R.138, C:R.138 NAD.7: 20 residues within 4Å: Chain D: F.7, G.8, K.9, F.10, H.14, G.16, H.17, L.20, G.36, R.41, E.81, P.86, Y.87, W.94, T.114, S.115, E.116, R.138, M.141 Ligands: PO4.8 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.87 Hydrogen bonds: D:F.7, D:K.9, D:F.10, D:G.36, D:R.41, D:Y.87, D:S.115, D:S.115, D:E.116, D:E.116, D:R.138, D:R.138, D:M.141 Salt bridges: D:K.9, D:H.17 pi-Cation interactions: D:R.138, D:R.138

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: H.14, H.17, R.138, S.144, G.145 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.138, A:G.145 Salt bridges: A:H.14 PO4.4: 5 residues within 4Å: Chain B: H.14, H.17, S.144, G.145 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.145 Salt bridges: B:H.14, B:H.17 PO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.8: 3 residues within 4Å: Chain D: S.144, G.145 Ligands: NAD.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, W.X. et al., CryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD. To Be Published

Release Date

2024-12-04

Peptides

Trifunctional NAD biosynthesis/regulator protein NadR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
G

D
J

Trifunctional NAD biosynthesis/regulator protein NadR