SMTL ID : 4k9c.1

CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE and 4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZINE-7-CARBOXYLIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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 11 PLIP interactions: 11 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 ADN.7: 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 14 PLIP interactions: 14 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, B:Y.180

2 x C29: 4-methyl-3,4-dihydro-2H-1,4-benzoxazine-7-carboxylic acid(Non-covalent)

C29.2: 6 residues within 4Å: Chain A: S.212, F.213, D.216, R.219, S.243, Q.246 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.246 Water bridges: A:T.247, A:T.247 Salt bridges: A:R.219 C29.8: 6 residues within 4Å: Chain B: S.212, F.213, D.216, R.219, S.243, Q.246 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.246 Salt bridges: B:R.219

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

DMS.3: 7 residues within 4Å: Chain A: I.38, A.65, E.66, Y.69, R.136 Ligands: DMS.4, 1Q8.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.136 Salt bridges: A:E.66 DMS.4: 8 residues within 4Å: Chain A: A.62, A.65, E.66, P.133, R.136, Y.152 Ligands: DMS.3, 1Q8.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.66, A:R.136 Salt bridges: A:E.66 DMS.9: 8 residues within 4Å: Chain B: I.38, A.65, E.66, Y.69, R.136, M.138 Ligands: DMS.10, 1Q8.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.136 Salt bridges: B:E.66 DMS.10: 6 residues within 4Å: Chain B: A.62, A.65, E.66, R.136 Ligands: DMS.9, 1Q8.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.136 Salt bridges: B:E.66

2 x 1Q8: N-(hydroxymethyl)benzamide(Non-covalent)

1Q8.5: 10 residues within 4Å: Chain A: I.38, Y.69, L.108, P.133, R.136 Chain B: Q.107, D.110, I.111 Ligands: DMS.3, DMS.4 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.38, A:Y.69, A:L.108, B:D.110, B:I.111 Hydrogen bonds: A:R.136, A:R.136, B:Q.107, B:D.110 Water bridges: A:D.106 1Q8.11: 9 residues within 4Å: Chain A: Q.107, D.110, I.111 Chain B: Y.69, L.108, P.133, R.136 Ligands: DMS.9, DMS.10 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.69, B:L.108, A:D.110, A:I.111 Hydrogen bonds: B:R.136, B:R.136, A:Q.107

2 x K: POTASSIUM ION(Non-covalent)

K.6: 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.12: 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 N-(HYDROXYMETHYL)BENZAMIDE and 4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZINE-7-CARBOXYLIC ACID. To be Published

Release Date

2013-05-22

Peptides

sugar kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

sugar kinase

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