SMTL ID : 4ycb.1

Structure of a single tryptophan mutant of Acetobacter aceti PurE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-octamer

Ligands

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: N.156, L.159, R.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.156, A:L.159 Water bridges: A:R.162 Salt bridges: A:R.162 ACT.5: 3 residues within 4Å: Chain B: N.156, A.158, R.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.156 Water bridges: B:R.162 Salt bridges: B:R.162 ACT.11: 3 residues within 4Å: Chain C: N.156, L.159, R.162 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.156, C:L.159 Water bridges: C:R.162 Salt bridges: C:R.162 ACT.15: 3 residues within 4Å: Chain D: N.156, A.158, R.162 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.156 Water bridges: D:R.162 Salt bridges: D:R.162 ACT.21: 3 residues within 4Å: Chain E: N.156, L.159, R.162 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.156, E:L.159 Water bridges: E:R.162 Salt bridges: E:R.162 ACT.25: 3 residues within 4Å: Chain F: N.156, A.158, R.162 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.156 Water bridges: F:R.162 Salt bridges: F:R.162 ACT.31: 3 residues within 4Å: Chain G: N.156, L.159, R.162 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:N.156, G:L.159 Water bridges: G:R.162 Salt bridges: G:R.162 ACT.35: 3 residues within 4Å: Chain H: N.156, A.158, R.162 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:N.156 Water bridges: H:R.162 Salt bridges: H:R.162

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

EDO.2: 6 residues within 4Å: Chain A: P.126 Chain F: G.30, S.31, D.34, A.85, G.86 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: G.137, A.138 Chain G: R.111 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain B: D.182, K.183 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: G.137, A.138 Chain F: R.111 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain C: P.126 Chain H: G.30, S.31, D.34, A.85, G.86 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain C: G.137, A.138 Chain E: R.111 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain D: D.182, K.183 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain D: G.137, A.138 Chain H: R.111 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain D: G.30, S.31, D.34, A.85, G.86 Chain E: P.126 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: R.111 Chain E: G.137, A.138 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain F: D.182, K.183 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain D: R.111 Chain F: G.137, A.138 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: G.30, S.31, D.34, A.85, G.86 Chain G: P.126 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: R.111 Chain G: G.137, A.138 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain H: D.182, K.183 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: R.111 Chain H: G.137, A.138 Ligand excluded by PLIP

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

SO4.4: 2 residues within 4Å: Chain A: K.142 Chain G: R.61 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain G Water bridges: A:K.142, A:K.142, A:K.142, A:K.142, A:K.142, G:R.61 Salt bridges: A:K.142, G:R.61 SO4.10: 2 residues within 4Å: Chain B: R.39, H.40 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.39, B:H.40 SO4.14: 2 residues within 4Å: Chain C: K.142 Chain E: R.61 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain C Water bridges: E:R.61, C:K.142, C:K.142, C:K.142, C:K.142, C:K.142 Salt bridges: E:R.61, C:K.142 SO4.20: 2 residues within 4Å: Chain D: R.39, H.40 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.39, D:H.40 SO4.24: 2 residues within 4Å: Chain A: R.61 Chain E: K.142 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Water bridges: E:K.142, E:K.142, E:K.142, E:K.142, E:K.142, A:R.61 Salt bridges: E:K.142, A:R.61 SO4.30: 2 residues within 4Å: Chain F: R.39, H.40 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.39, F:H.40 SO4.34: 2 residues within 4Å: Chain C: R.61 Chain G: K.142 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain G Water bridges: C:R.61, G:K.142, G:K.142, G:K.142, G:K.142, G:K.142 Salt bridges: C:R.61, G:K.142 SO4.40: 2 residues within 4Å: Chain H: R.39, H.40 2 PLIP interactions: 2 interactions with chain H Salt bridges: H:R.39, H:H.40

4 x K: POTASSIUM ION(Non-covalent)

K.8: 2 residues within 4Å: Chain B: P.175 Ligands: PGF.9 No protein-ligand interaction detected (PLIP) K.18: 2 residues within 4Å: Chain D: P.175 Ligands: PGF.19 No protein-ligand interaction detected (PLIP) K.28: 2 residues within 4Å: Chain F: P.175 Ligands: PGF.29 No protein-ligand interaction detected (PLIP) K.38: 2 residues within 4Å: Chain H: P.175 Ligands: PGF.39 No protein-ligand interaction detected (PLIP)

4 x PGF: 2,5,8,11-TETRAOXATRIDECANE(Non-covalent)

PGF.9: 6 residues within 4Å: Chain B: A.172, S.173, V.174, P.175, N.176 Ligands: K.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.176 PGF.19: 6 residues within 4Å: Chain D: A.172, S.173, V.174, P.175, N.176 Ligands: K.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.176 PGF.29: 6 residues within 4Å: Chain F: A.172, S.173, V.174, P.175, N.176 Ligands: K.28 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.176 PGF.39: 6 residues within 4Å: Chain H: A.172, S.173, V.174, P.175, N.176 Ligands: K.38 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sullivan, K.L. et al., Structure of a single tryptophan mutant of Acetobacter aceti PurE. To Be Published

Release Date

2016-02-24

Peptides

N5-carboxyaminoimidazole ribonucleotide mutase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

N5-carboxyaminoimidazole ribonucleotide mutase

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