SMTL ID : 4kad.1

Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N1-(2.3-dihydro-1H-inden-5-yl)acetam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ADN: ADENOSINE(Non-covalent)

ADN.1: 19 residues within 4Å: Chain A: N.33, I.35, D.37, M.57, G.80, G.81, S.82, N.85, S.137, I.139, M.149, T.151, L.153, E.178, Y.180, T.296, G.297, D.300, P.336 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.33, A:D.37, A:G.81, A:S.82, A:N.85, A:G.297 Water bridges: A:R.147, A:R.147, A:R.147, A:D.300, A:D.300 pi-Stacking: A:Y.180, A:Y.180 ADN.6: 19 residues within 4Å: Chain B: N.33, I.35, D.37, M.57, G.80, G.81, S.82, N.85, S.137, I.139, M.149, T.151, L.153, E.178, Y.180, T.296, G.297, D.300, P.336 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.33, B:D.37, B:G.81, B:S.82, B:N.85, B:T.151, B:G.297 Water bridges: B:R.147, B:R.147, B:R.147, B:G.297, B:D.300 pi-Stacking: B:Y.180

2 x 1QB: N-(4,7-dihydro-1H-inden-6-yl)acetamide(Non-covalent)

1QB.2: 10 residues within 4Å: Chain A: T.267, S.269, E.270, G.272, A.286, I.287, I.289, A.298, A.327, I.331 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.270, A:A.286, A:I.289, A:I.331 Water bridges: A:S.269, A:C.324, A:G.328 1QB.7: 9 residues within 4Å: Chain B: S.269, E.270, G.272, A.286, I.289, V.292, C.324, A.327, I.331 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.270, B:A.286, B:I.289, B:V.292, B:I.331 Water bridges: B:C.324, B:G.328

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: I.38, A.65, E.66, Y.69, R.136 Ligands: DMS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.136 Salt bridges: A:E.66 DMS.4: 6 residues within 4Å: Chain A: A.62, A.65, E.66, R.136, Y.152 Ligands: DMS.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.66, A:R.136 DMS.8: 6 residues within 4Å: Chain B: I.38, A.65, E.66, Y.69, R.136 Ligands: DMS.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.136 DMS.9: 7 residues within 4Å: Chain B: A.62, A.65, E.66, P.133, R.136, Y.152 Ligands: DMS.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.136 Water bridges: B:R.136

2 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: D.294, T.296, V.330, Q.333, G.335 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.294, A:T.296, A:V.330, A:Q.333, A:G.335 K.10: 5 residues within 4Å: Chain B: D.294, T.296, V.330, Q.333, G.335 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.294, B:T.296, B:V.330, B:Q.333, B:G.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.N. et al., Crystal structure of probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N1-(2.3-dihydro-1H-inden-5-yl)acetam. To be Published

Release Date

2013-05-22

Peptides

Probable sugar kinase protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable sugar kinase protein

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