SMTL ID : 5zol.1

Crystal structure of a three sites mutantion of FSAA complexed with HA and product

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-10-mer

Ligands

10 x 4Y8: 1-hydroxypropan-2-one(Covalent)

4Y8.1: 7 residues within 4Å: Chain A: D.41, T.61, T.62, N.63, K.120, A.164 Ligands: LW2.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.120, A:A.164 Hydrogen bonds: A:D.41, A:N.63 Water bridges: A:D.41 4Y8.5: 8 residues within 4Å: Chain B: D.41, T.61, T.62, N.63, K.120, T.144, A.164 Ligands: LW2.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.120, B:A.164 Hydrogen bonds: B:D.41, B:N.63 Water bridges: B:N.63 4Y8.8: 8 residues within 4Å: Chain C: D.41, T.61, T.62, N.63, K.120, T.144, A.164 Ligands: LW2.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.120, C:A.164 Hydrogen bonds: C:D.41, C:N.63 Water bridges: C:D.41, C:K.120 4Y8.11: 8 residues within 4Å: Chain D: D.41, T.61, T.62, N.63, K.120, T.144, A.164 Ligands: LW2.12 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.120, D:A.164 Hydrogen bonds: D:D.41, D:T.61, D:N.63 Water bridges: D:D.41 4Y8.14: 8 residues within 4Å: Chain E: D.41, T.61, T.62, N.63, K.120, T.144, A.164 Ligands: LW2.15 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:K.120, E:A.164 Hydrogen bonds: E:D.41, E:T.61, E:N.63 Water bridges: E:D.41 4Y8.17: 6 residues within 4Å: Chain F: D.41, T.61, T.62, N.63, K.120, A.164 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:K.120, F:A.164 Hydrogen bonds: F:D.41, F:T.61, F:N.63, F:K.120 Water bridges: F:N.63 4Y8.21: 8 residues within 4Å: Chain G: D.41, T.61, T.62, N.63, K.120, T.144, A.164 Ligands: LW1.22 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:K.120, G:A.164 Hydrogen bonds: G:D.41, G:T.61, G:N.63 Water bridges: G:N.63, G:K.120 4Y8.24: 7 residues within 4Å: Chain H: D.41, T.61, T.62, N.63, K.120, T.144, A.164 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:K.120, H:A.164 Hydrogen bonds: H:D.41, H:N.63 Water bridges: H:N.63 4Y8.27: 6 residues within 4Å: Chain I: D.41, T.61, N.63, K.120, T.144, A.164 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:N.63, I:K.120 4Y8.31: 8 residues within 4Å: Chain J: D.41, T.61, T.62, N.63, K.120, T.144, A.164 Ligands: LW2.32 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:K.120, J:A.164 Hydrogen bonds: J:D.41, J:N.63 Water bridges: J:N.63

9 x LW2: (3S,4S)-3,4-dihydroxy-4-(thiophen-2-yl)butan-2-one(Non-covalent)

LW2.2: 8 residues within 4Å: Chain A: D.41, N.63, Y.166, N.168, R.169, S.201 Chain B: F.242 Ligands: 4Y8.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.166, B:F.242 Hydrogen bonds: A:D.41, A:N.63, A:R.169 Water bridges: A:S.201 LW2.6: 6 residues within 4Å: Chain B: D.41, N.63, Y.166, R.169, S.201 Ligands: 4Y8.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.166 Hydrogen bonds: B:D.41, B:N.63, B:S.201 pi-Cation interactions: B:R.169 LW2.9: 9 residues within 4Å: Chain C: D.41, N.63, Y.166, N.168, R.169, S.201, F.202, K.203 Ligands: 4Y8.8 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.166 Hydrogen bonds: C:D.41, C:N.63, C:R.169 Water bridges: C:S.201 LW2.12: 7 residues within 4Å: Chain D: D.41, N.63, Y.166, R.169, S.201, K.203 Ligands: 4Y8.11 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.166 Hydrogen bonds: D:D.41, D:N.63 Water bridges: D:S.201 LW2.15: 8 residues within 4Å: Chain E: D.41, N.63, Y.166, N.168, R.169, S.201, K.203 Ligands: 4Y8.14 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.166 Hydrogen bonds: E:N.63, E:R.169 pi-Cation interactions: E:R.169 LW2.18: 6 residues within 4Å: Chain F: D.41, Y.166, N.168, R.169, S.201, K.203 3 PLIP interactions: 3 interactions with chain F Water bridges: F:D.41, F:S.201, F:S.201 LW2.25: 4 residues within 4Å: Chain H: D.41, Y.166, R.169, S.201 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:Y.166 Hydrogen bonds: H:S.201 Water bridges: H:S.201, H:F.202 LW2.28: 6 residues within 4Å: Chain I: D.41, N.63, Y.166, R.169, S.201, K.203 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:Y.166, I:R.169 Hydrogen bonds: I:N.63 pi-Cation interactions: I:K.203 LW2.32: 7 residues within 4Å: Chain J: D.41, N.63, Y.166, R.169, S.201, K.203 Ligands: 4Y8.31 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:Y.166 Hydrogen bonds: J:D.41, J:N.63 Water bridges: J:S.201

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

CL.3: 2 residues within 4Å: Chain A: T.42, L.223 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: R.111, P.140 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain F: T.42, S.43, T.66 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain I: R.111, P.140 Ligand excluded by PLIP

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

SO4.4: 4 residues within 4Å: Chain A: A.97, T.98, T.99, G.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.98, A:T.99 SO4.7: 4 residues within 4Å: Chain B: A.97, T.98, T.99, G.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.98, B:T.99, B:T.99, B:G.102 SO4.13: 4 residues within 4Å: Chain D: A.97, T.98, T.99, G.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.98, D:T.98, D:T.99 SO4.16: 3 residues within 4Å: Chain E: R.252, T.253, S.254 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.253 SO4.20: 4 residues within 4Å: Chain F: A.97, T.98, T.99, G.102 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.98, F:T.98, F:T.99, F:G.102 SO4.23: 4 residues within 4Å: Chain G: A.97, T.98, T.99, G.102 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:T.98, G:T.98, G:T.99, G:T.99, G:G.102 SO4.26: 4 residues within 4Å: Chain H: A.97, T.98, T.99, G.102 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:T.98, H:T.99, H:G.102 SO4.30: 4 residues within 4Å: Chain I: A.97, T.98, T.99, G.102 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:T.98, I:T.98, I:T.99 SO4.33: 4 residues within 4Å: Chain J: A.97, T.98, T.99, G.102 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:T.98, J:T.99, J:G.102

1 x LW1: thiophene-2-carbaldehyde(Non-covalent)

LW1.22: 5 residues within 4Å: Chain G: D.41, N.63, R.169, S.201 Ligands: 4Y8.21 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., The engineering of decameric d-fructose-6-phosphate aldolase A by combinatorial modulation of inter- and intra-subunit interactions. Chem.Commun.(Camb.) (2020)

Release Date

2019-06-12

Peptides

Fructose-6-phosphate aldolase 1: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Fructose-6-phosphate aldolase 1