SMTL ID : 1y3i.1 (1 other biounit)

Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain B: L.228, F.229, G.230, R.231 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.230, B:R.231, C:R.231 Salt bridges: B:R.231 SO4.8: 4 residues within 4Å: Chain D: L.228, F.229, G.230, R.231 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:R.231, D:G.230, D:R.231 Salt bridges: D:R.231

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

NAD.2: 19 residues within 4Å: Chain A: D.85, G.86, L.89, R.109, I.110, F.112, L.113, N.159, E.160, T.197, T.200, A.201, Y.202, S.205, D.257 Chain C: V.171, D.189, N.224, H.226 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.202, A:Y.202 Hydrogen bonds: A:D.85, A:R.109, A:I.110, A:N.159, A:E.160, A:T.197, A:T.200, A:Y.202, A:S.205, C:V.171, C:D.189, C:N.224 NAD.3: 20 residues within 4Å: Chain B: D.85, G.86, L.89, R.109, F.112, L.113, N.159, E.160, G.198, T.200, A.201, Y.202, S.205, D.257, G.258 Chain D: G.170, V.171, D.189, N.224, H.226 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:Y.202, D:V.171 Hydrogen bonds: B:R.109, B:R.109, B:N.159, B:N.159, B:E.160, B:Y.202, B:S.205, B:D.257, D:V.171, D:V.171, D:N.224 NAD.9: 19 residues within 4Å: Chain A: V.171, D.189, N.224, H.226 Chain C: D.85, G.86, L.89, R.109, I.110, F.112, L.113, N.159, E.160, T.197, T.200, A.201, Y.202, S.205, D.257 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.202, C:Y.202 Hydrogen bonds: C:D.85, C:R.109, C:I.110, C:N.159, C:E.160, C:T.197, C:T.200, C:Y.202, C:S.205, A:V.171, A:D.189, A:N.224 NAD.10: 20 residues within 4Å: Chain B: G.170, V.171, D.189, N.224, H.226 Chain D: D.85, G.86, L.89, R.109, F.112, L.113, N.159, E.160, G.198, T.200, A.201, Y.202, S.205, D.257, G.258 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:Y.202, B:V.171 Hydrogen bonds: D:R.109, D:R.109, D:N.159, D:N.159, D:E.160, D:Y.202, D:S.205, D:D.257, B:V.171, B:V.171, B:N.224

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.5: 6 residues within 4Å: Chain A: H.226, A.227, L.228 Chain C: F.204, K.296, F.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.227 GOL.6: 3 residues within 4Å: Chain A: G.207 Chain B: R.231 Ligands: GOL.13 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:A.206, B:R.231, B:R.231 Water bridges: C:G.230, A:G.207 GOL.7: 5 residues within 4Å: Chain B: H.226, A.227, L.228 Chain D: F.297, R.298 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.298, B:H.226 Water bridges: D:R.298, D:R.298 GOL.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.12: 6 residues within 4Å: Chain A: F.204, K.296, F.297 Chain C: H.226, A.227, L.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.227 GOL.13: 3 residues within 4Å: Chain C: G.207 Chain D: R.231 Ligands: GOL.6 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 interactions with chain D Water bridges: C:G.207, A:G.230 Hydrogen bonds: A:A.206, D:R.231, D:R.231 GOL.14: 5 residues within 4Å: Chain B: F.297, R.298 Chain D: H.226, A.227, L.228 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.298, D:H.226 Water bridges: B:R.298, B:R.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mori, S. et al., NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex. Biochem.Biophys.Res.Commun. (2005)

Release Date

2005-01-18

Peptides

Inorganic polyphosphate/ATP-NAD kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Inorganic polyphosphate/ATP-NAD kinase

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