SMTL ID : 1k4m.1

Crystal structure of E.coli nicotinic acid mononucleotide adenylyltransferase complexed to deamido-NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: F.8, G.9, G.10, T.11, F.12, H.16, G.18, H.19, N.40, H.45, R.46, Y.84, T.85, F.104, I.106, G.107, D.109, S.110, W.117, Y.118, R.133, R.134, F.177, I.179 Ligands: CIT.2 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:H.45, A:W.117 Hydrogen bonds: A:G.9, A:T.11, A:F.12, A:N.40, A:T.85, A:T.85, A:T.85, A:G.107, A:S.110, A:S.110, A:S.110, A:Y.118, A:F.177, A:I.179 Water bridges: A:G.9, A:G.10, A:G.10, A:D.13, A:H.19, A:N.40, A:H.45, A:R.134, A:R.134, A:R.134, A:R.134, A:F.177 Salt bridges: A:H.19, A:H.45, A:R.46, A:R.46 pi-Stacking: A:H.45, A:W.117, A:W.117 NAD.3: 25 residues within 4Å: Chain B: F.8, G.9, G.10, T.11, F.12, H.16, G.18, H.19, N.40, H.45, R.46, Y.84, T.85, F.104, I.106, G.107, D.109, S.110, W.117, Y.118, R.133, R.134, F.177, I.179 Ligands: CIT.4 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:G.9, B:T.11, B:F.12, B:N.40, B:T.85, B:T.85, B:T.85, B:G.107, B:S.110, B:S.110, B:S.110, B:Y.118, B:I.179 Water bridges: B:G.10, B:G.10, B:T.11, B:D.13, B:H.19, B:H.45, B:H.45, B:R.46, B:R.46, B:I.105, B:D.109, B:R.134, B:R.134, B:F.177, B:I.179 Salt bridges: B:H.19, B:H.45, B:R.46, B:R.46 pi-Stacking: B:H.45, B:W.117, B:W.117 NAD.5: 24 residues within 4Å: Chain C: F.8, G.9, G.10, T.11, F.12, H.16, G.18, H.19, N.40, H.45, R.46, Y.84, T.85, F.104, I.106, G.107, D.109, S.110, W.117, Y.118, R.133, R.134, F.177, I.179 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:W.117 Hydrogen bonds: C:G.9, C:T.11, C:F.12, C:N.40, C:T.85, C:T.85, C:T.85, C:G.107, C:S.110, C:S.110, C:S.110, C:Y.118, C:F.177 Water bridges: C:G.10, C:G.10, C:T.11, C:D.13, C:H.45, C:A.86, C:I.105, C:D.109, C:R.134, C:R.134, C:F.177, C:I.179 Salt bridges: C:H.19, C:H.45, C:R.46, C:R.46 pi-Stacking: C:W.117, C:W.117

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 9 residues within 4Å: Chain A: D.13, R.46, D.109, R.134, S.180, A.181, T.182, R.185 Ligands: NAD.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.181, A:T.182, A:T.182, A:T.182 Water bridges: A:R.46, A:R.46, A:R.46, A:R.46, A:R.46, A:R.134, A:R.134, A:S.180, A:S.180, A:T.182, A:R.185 Salt bridges: A:R.46, A:R.134, A:R.185 CIT.4: 8 residues within 4Å: Chain B: R.46, D.109, R.134, S.180, A.181, T.182, R.185 Ligands: NAD.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:A.181, B:T.182, B:T.182, B:T.182 Water bridges: B:D.13, B:R.46, B:R.46, B:R.46, B:D.109, B:D.109, B:R.134, B:R.185 Salt bridges: B:R.46, B:R.134, B:R.185 CIT.6: 7 residues within 4Å: Chain C: R.46, D.109, R.134, S.180, A.181, T.182, R.185 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:A.181, C:T.182, C:T.182, C:T.182 Water bridges: C:R.46, C:R.46, C:R.46, C:R.46, C:D.109, C:D.109, C:R.134, C:R.134 Salt bridges: C:R.46, C:R.134, C:R.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Structure (2002)

Release Date

2002-10-08

Peptides

NaMN adenylyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

NaMN adenylyltransferase

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