SMTL ID : 4ybr.1

Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 22 residues within 4Å: Chain A: M.10, G.11, G.12, T.13, F.14, H.18, H.21, S.42, T.85, T.87, F.105, T.106, T.107, G.108, A.111, I.115, W.118, Q.119, V.133, L.165, S.168, S.169 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.115 Hydrogen bonds: A:G.11, A:G.11, A:T.13, A:T.13, A:S.42, A:S.42, A:T.87, A:T.107, A:G.108, A:W.118, A:Q.119, A:S.169, A:S.169 Water bridges: A:G.12, A:G.12, A:F.14, A:F.14, A:D.110, A:T.170, A:T.170, A:R.173, A:R.173 Salt bridges: A:H.18, A:H.21 pi-Stacking: A:H.21 NAP.4: 24 residues within 4Å: Chain B: M.10, G.11, G.12, T.13, F.14, H.18, H.21, S.42, R.50, T.85, Y.86, T.87, F.105, T.106, T.107, G.108, A.111, I.115, V.133, R.135, L.165, S.168, S.169 Ligands: SO4.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.115 Hydrogen bonds: B:G.11, B:G.11, B:T.13, B:T.13, B:S.42, B:T.87, B:T.87, B:T.107, B:G.108, B:R.135, B:S.169, B:S.169 Water bridges: B:G.12, B:G.12, B:F.14, B:F.14, B:Y.138, B:T.170, B:T.170, B:R.173, B:R.173, B:R.173 Salt bridges: B:H.18, B:H.21, B:R.50, B:R.50 pi-Stacking: B:H.21

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 7 residues within 4Å: Chain A: W.183, Y.184, D.188 Chain B: S.68, N.69, P.70, R.71 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.68 Water bridges: B:Y.19, B:Y.19, B:R.71, B:R.71, A:Y.19 Salt bridges: B:R.71, A:D.188, A:D.188 EPE.5: 7 residues within 4Å: Chain A: S.68, N.69, P.70, R.71 Chain B: W.183, Y.184, D.188 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.68 Water bridges: A:R.71 Salt bridges: B:D.188, B:D.188

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

SO4.3: 5 residues within 4Å: Chain A: R.141, N.142, E.143, H.144, I.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.142, A:H.144, A:I.145 Water bridges: A:E.143 SO4.6: 5 residues within 4Å: Chain B: R.135, Y.138, S.168, T.170 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.170 Water bridges: B:R.135, B:R.135, B:S.168, B:T.170 Salt bridges: B:R.135

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

CL.7: 1 residues within 4Å: Chain B: G.83 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.5, H.98, D.100, S.101 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korotkov, K.V., Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212. to be published

Release Date

2016-02-03

Peptides

Nicotinate-nucleotide adenylyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinate-nucleotide adenylyltransferase

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