SMTL ID : 3oi7.1 (1 other biounit)

Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x OI7: 1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose(Non-covalent)

OI7.1: 14 residues within 4Å: Chain A: R.33, S.40, Q.44, Y.45, T.46, R.90, E.120, Y.123, H.197, G.198, H.199, R.202 Chain B: H.265 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.46, A:E.120, A:Y.123, A:Y.123, A:G.198, A:H.199, A:H.199 Water bridges: A:S.40 Salt bridges: A:R.33, A:R.90, A:H.197, A:H.199, A:R.202, B:H.265 OI7.7: 15 residues within 4Å: Chain A: H.265 Chain B: R.33, S.40, Q.44, Y.45, T.46, R.90, E.120, Y.123, H.197, G.198, H.199, R.202 Ligands: MG.8, NA.9 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.33, B:Q.44, B:T.46, B:Y.123, B:G.198, B:H.199, B:H.199 Water bridges: B:T.46, B:T.46 Salt bridges: B:R.33, B:R.90, B:H.197, B:H.199, B:R.202, A:H.265

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.37, S.40, T.46, R.90 Ligands: OI7.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:T.37, OI7.1 MG.8: 4 residues within 4Å: Chain B: T.37, T.46, R.90 Ligands: OI7.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:T.37, OI7.7

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: R.175, N.178, L.179, V.234, P.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.175, A:N.178, A:L.179 NA.9: 5 residues within 4Å: Chain B: R.33, A.34, G.35, S.40 Ligands: OI7.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.34, B:S.40 NA.10: 4 residues within 4Å: Chain B: T.37, E.38, P.52, T.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.38, B:P.52

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: L.48, P.87, R.88, D.116, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.88, A:R.88, A:D.116 EDO.5: 6 residues within 4Å: Chain A: Q.36, S.40, K.41, Q.60, D.254, A.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.40, A:Q.60 EDO.11: 5 residues within 4Å: Chain B: L.48, P.87, R.88, D.116, R.119 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.88, B:R.88 EDO.12: 1 residues within 4Å: Chain B: R.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.132

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: D.96, R.107 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clasquin, M.F. et al., Riboneogenesis in yeast. Cell(Cambridge,Mass.) (2011)

Release Date

2010-11-17

Peptides

Uncharacterized protein YKR043C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Uncharacterized protein YKR043C

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