SMTL ID : 1lw7.1

NADR PROTEIN FROM HAEMOPHILUS INFLUENZAE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.10, S.146, A.147, T.148, R.151 Ligands: NAD.6 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: R.166, H.240 Ligands: SO4.23 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: K.163, Y.236, R.239, H.240 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.232 Ligands: NAD.7 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: N.188, W.200 Ligands: NAD.7 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain B: K.10, S.146, A.147, T.148, R.151 Ligands: NAD.13 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: R.166, H.240 Ligands: SO4.16 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: K.163, Y.236, R.239, H.240 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: R.232 Ligands: NAD.14 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: N.188, W.200 Ligands: NAD.14 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain C: K.10, S.146, A.147, T.148, R.151 Ligands: NAD.20 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain C: R.166, H.240 Ligands: SO4.9 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: K.163, Y.236, R.239, H.240 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: R.232 Ligands: NAD.21 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: N.188, W.200 Ligands: NAD.21 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain D: K.10, S.146, A.147, T.148, R.151 Ligands: NAD.27 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: R.166, H.240 Ligands: SO4.2 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain D: K.163, Y.236, R.239, H.240 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain D: R.232 Ligands: NAD.28 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: N.188, W.200 Ligands: NAD.28 Ligand excluded by PLIP

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

NAD.6: 26 residues within 4Å: Chain A: F.8, G.9, K.10, F.11, H.15, H.18, M.21, C.37, R.42, E.83, I.86, P.87, S.88, Y.89, N.91, G.92, W.93, W.96, S.116, S.117, E.118, D.137, R.140, F.143, V.145 Ligands: SO4.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.96 Hydrogen bonds: A:F.8, A:K.10, A:F.11, A:H.18, A:R.42, A:R.42, A:P.87, A:S.117, A:S.117, A:S.117, A:E.118, A:R.140, A:R.140, A:F.143, A:V.145 Salt bridges: A:K.10, A:K.10, A:H.18 pi-Stacking: A:Y.89, A:W.93, A:W.93, A:W.96, A:W.96 pi-Cation interactions: A:R.140, A:R.140 NAD.7: 10 residues within 4Å: Chain A: S.198, A.199, W.200, Y.233, Y.236, A.237 Chain B: K.70 Chain D: Y.71 Ligands: SO4.4, SO4.5 12 PLIP interactions: 1 interactions with chain D, 9 interactions with chain A, 2 interactions with chain B Salt bridges: D:K.70, B:K.70, B:K.70 Hydrophobic interactions: A:W.200 Hydrogen bonds: A:S.198, A:S.198, A:W.200, A:A.237 pi-Stacking: A:W.200, A:Y.233, A:Y.236, A:Y.236 NAD.13: 26 residues within 4Å: Chain B: F.8, G.9, K.10, F.11, H.15, H.18, M.21, C.37, R.42, E.83, I.86, P.87, S.88, Y.89, N.91, G.92, W.93, W.96, S.116, S.117, E.118, D.137, R.140, F.143, V.145 Ligands: SO4.8 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:W.96 Hydrogen bonds: B:F.8, B:K.10, B:F.11, B:H.18, B:R.42, B:R.42, B:P.87, B:S.117, B:S.117, B:S.117, B:E.118, B:R.140, B:R.140, B:F.143, B:V.145 Salt bridges: B:K.10, B:K.10, B:H.18 pi-Stacking: B:Y.89, B:W.93, B:W.93, B:W.96, B:W.96 pi-Cation interactions: B:R.140, B:R.140 NAD.14: 10 residues within 4Å: Chain A: K.70 Chain B: S.198, A.199, W.200, Y.233, Y.236, A.237 Chain C: Y.71 Ligands: SO4.11, SO4.12 12 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:W.200 Hydrogen bonds: B:S.198, B:S.198, B:W.200, B:A.237 pi-Stacking: B:W.200, B:Y.233, B:Y.236, B:Y.236 Salt bridges: A:K.70, A:K.70, C:K.70 NAD.20: 26 residues within 4Å: Chain C: F.8, G.9, K.10, F.11, H.15, H.18, M.21, C.37, R.42, E.83, I.86, P.87, S.88, Y.89, N.91, G.92, W.93, W.96, S.116, S.117, E.118, D.137, R.140, F.143, V.145 Ligands: SO4.15 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:W.96 Hydrogen bonds: C:F.8, C:K.10, C:F.11, C:R.42, C:R.42, C:P.87, C:S.117, C:S.117, C:S.117, C:D.137, C:R.140, C:R.140, C:F.143, C:V.145 Salt bridges: C:K.10, C:K.10, C:H.18 pi-Stacking: C:Y.89, C:W.93, C:W.93, C:W.96, C:W.96 pi-Cation interactions: C:R.140, C:R.140 NAD.21: 10 residues within 4Å: Chain B: Y.71 Chain C: S.198, A.199, W.200, Y.233, Y.236, A.237 Chain D: K.70 Ligands: SO4.18, SO4.19 13 PLIP interactions: 2 interactions with chain D, 10 interactions with chain C, 1 interactions with chain B Salt bridges: D:K.70, D:K.70, B:K.70 Hydrophobic interactions: C:W.200 Hydrogen bonds: C:S.198, C:S.198, C:W.200, C:Y.233, C:A.237 pi-Stacking: C:W.200, C:Y.233, C:Y.236, C:Y.236 NAD.27: 26 residues within 4Å: Chain D: F.8, G.9, K.10, F.11, H.15, H.18, M.21, C.37, R.42, E.83, I.86, P.87, S.88, Y.89, N.91, G.92, W.93, W.96, S.116, S.117, E.118, D.137, R.140, F.143, V.145 Ligands: SO4.22 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:W.96 Hydrogen bonds: D:F.8, D:K.10, D:F.11, D:R.42, D:R.42, D:P.87, D:S.117, D:S.117, D:S.117, D:D.137, D:R.140, D:R.140, D:F.143, D:V.145 Salt bridges: D:K.10, D:K.10, D:H.18 pi-Stacking: D:Y.89, D:W.93, D:W.93, D:W.96, D:W.96 pi-Cation interactions: D:R.140, D:R.140 NAD.28: 10 residues within 4Å: Chain A: Y.71 Chain C: K.70 Chain D: S.198, A.199, W.200, Y.233, Y.236, A.237 Ligands: SO4.25, SO4.26 13 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:W.200 Hydrogen bonds: D:S.198, D:S.198, D:W.200, D:Y.233, D:A.237 pi-Stacking: D:W.200, D:Y.233, D:Y.236, D:Y.236 Salt bridges: A:K.70, C:K.70, C:K.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S.K. et al., Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities. J.Biol.Chem. (2002)

Release Date

2002-08-07

Peptides

TRANSCRIPTIONAL REGULATOR NADR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

TRANSCRIPTIONAL REGULATOR NADR