SMTL ID : 3e18.1

CRYSTAL STRUCTURE OF NAD-BINDING PROTEIN FROM Listeria innocua

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.190 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: D.190 No protein-ligand interaction detected (PLIP)

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

CL.2: 4 residues within 4Å: Chain A: R.346, T.347 Chain B: R.346, T.347 Ligand excluded by PLIP

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

NAD.3: 26 residues within 4Å: Chain A: V.11, G.12, Y.13, G.14, G.15, M.16, F.36, D.37, I.38, L.39, K.42, A.72, T.73, P.74, N.75, H.78, E.95, K.96, P.97, H.122, N.124, D.162, W.163, R.164, H.180 Ligands: GOL.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:M.16 Hydrogen bonds: A:Y.13, A:G.15, A:M.16, A:I.38, A:N.75, A:H.78, A:K.96, A:H.122, A:N.124, A:N.124 Water bridges: A:G.14, A:G.17, A:K.42, A:K.42, A:N.75 Salt bridges: A:K.42, A:R.164 pi-Cation interactions: A:K.96 NAD.11: 24 residues within 4Å: Chain B: V.11, G.12, Y.13, G.14, G.15, M.16, D.37, I.38, L.39, K.42, A.72, T.73, P.74, N.75, H.78, E.95, K.96, P.97, H.122, N.124, W.163, R.164, D.176, H.180 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:M.16 Hydrogen bonds: B:G.15, B:M.16, B:I.38, B:K.42, B:T.73, B:N.75, B:E.95, B:K.96, B:N.124, B:D.176 Water bridges: B:G.14, B:G.17, B:K.42, B:N.75, B:D.162, B:D.162 Salt bridges: B:K.42, B:R.164 pi-Cation interactions: B:K.96

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: F.147, H.148, K.242 Chain B: S.201, V.213 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.201, A:K.242 Water bridges: B:F.212, B:E.227, B:E.227, A:H.148, A:K.242 GOL.5: 7 residues within 4Å: Chain A: K.96, R.125, R.164, D.176, W.177, H.180 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.125, A:R.125, A:R.164, A:R.164, A:H.180 GOL.6: 4 residues within 4Å: Chain A: H.251, G.257, E.258 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.251, A:G.257 GOL.7: 5 residues within 4Å: Chain A: E.258, T.294, L.295, S.296 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.258, A:S.296 GOL.8: 9 residues within 4Å: Chain A: R.152, V.153, H.154, K.235, L.236, P.237, R.238, D.252, W.253 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.154, A:L.236, A:D.252, A:D.252, A:W.253 Water bridges: A:R.238, A:R.238 GOL.9: 5 residues within 4Å: Chain A: A.112, K.113, N.116, K.117, H.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.116 Water bridges: A:M.109, A:K.113 GOL.12: 6 residues within 4Å: Chain A: F.147, G.243, T.244 Chain B: A.203, T.231, F.233 No protein-ligand interaction detected (PLIP) GOL.13: 2 residues within 4Å: Chain B: R.43, E.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.43, B:E.44 GOL.14: 5 residues within 4Å: Chain B: K.235, L.236, P.237, H.251, D.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.251, B:D.252 Water bridges: B:K.235 GOL.15: 3 residues within 4Å: Chain B: M.146, N.220, G.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., CRYSTAL STRUCTURE OF NAD-BINDING PROTEIN FROM Listeria innocua. To be Published

Release Date

2008-08-12

Peptides

oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

oxidoreductase