SMTL ID : 4u4m.1

Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-tetramer

Ligands

10 x URE: UREA(Non-functional Binders)

URE.1: 6 residues within 4Å: Chain A: S.45, G.46, F.136, T.165, F.254 Ligands: PYR.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.46 URE.2: 6 residues within 4Å: Chain A: D.167, Y.192, D.194, P.245 Chain C: A.170, R.173 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.173, A:D.194 URE.3: 5 residues within 4Å: Chain A: N.82, R.84, E.85, E.88 Chain B: E.56 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.53, A:N.82, A:E.88, A:E.88 URE.9: 6 residues within 4Å: Chain A: W.109 Chain B: G.191, Y.192, A.210, F.254 Ligands: PYR.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.191, B:A.210 URE.10: 2 residues within 4Å: Chain B: R.62, D.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.66 URE.11: 4 residues within 4Å: Chain B: Q.19, L.20, E.56, A.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.20, B:E.56 URE.12: 5 residues within 4Å: Chain A: R.118 Chain B: D.251, S.278, P.279, D.281 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.278, B:S.278, B:D.281, A:R.118 URE.17: 3 residues within 4Å: Chain C: E.260, V.263, K.285 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.260, C:E.260, C:K.285 URE.19: 6 residues within 4Å: Chain D: Y.134, F.136, T.165, G.191, F.254 Ligands: PYR.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.134, D:Y.134, D:G.191 Water bridges: D:A.210 URE.20: 5 residues within 4Å: Chain C: R.118 Chain D: D.251, S.278, P.279, D.281 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.278, D:P.279, D:D.281, C:R.118, C:R.118

4 x PYR: PYRUVIC ACID(Covalent)

PYR.4: 10 residues within 4Å: Chain A: P.9, F.41, G.44, S.45, G.46, Y.134, K.163, G.191, I.208 Ligands: URE.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.9, A:P.9, A:K.163, A:I.208 Hydrogen bonds: A:S.45, A:G.46, A:Y.134 Salt bridges: A:K.163 PYR.13: 9 residues within 4Å: Chain B: P.9, F.41, G.44, S.45, G.46, Y.134, K.163, I.208 Ligands: URE.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.9, B:P.9, B:K.163 Hydrogen bonds: B:S.45, B:G.46, B:Y.134 Salt bridges: B:K.163 PYR.18: 9 residues within 4Å: Chain C: P.9, F.41, G.44, S.45, G.46, Y.134, K.163, G.191, I.208 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.9, C:K.163 Hydrogen bonds: C:S.45, C:G.46, C:Y.134 Salt bridges: C:K.163 PYR.21: 10 residues within 4Å: Chain D: P.9, F.41, G.44, S.45, G.46, Y.134, K.163, G.191, I.208 Ligands: URE.19 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.9, D:P.9, D:K.163 Hydrogen bonds: D:S.45, D:G.46 Salt bridges: D:K.163

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

EDO.5: 2 residues within 4Å: Chain A: A.170, H.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 10 residues within 4Å: Chain A: L.43, G.44, F.49, R.57, G.77, G.79, V.102, V.103, I.104, Y.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.57, A:T.78, A:G.79, A:V.102, A:I.104 EDO.8: 2 residues within 4Å: Chain A: A.96, G.97 No protein-ligand interaction detected (PLIP) EDO.14: 9 residues within 4Å: Chain B: L.43, G.44, F.49, G.77, T.78, G.79, V.102, V.103, I.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.43, B:T.78, B:G.79, B:I.104 EDO.15: 5 residues within 4Å: Chain A: R.84 Chain B: G.18, H.272, L.274, P.275 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.272 EDO.16: 4 residues within 4Å: Chain B: K.180, P.184, G.203, D.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.180, B:P.184 EDO.22: 2 residues within 4Å: Chain D: K.150, D.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.150, D:D.154 EDO.23: 2 residues within 4Å: Chain D: A.1, H.185 No protein-ligand interaction detected (PLIP) EDO.24: 3 residues within 4Å: Chain D: G.36, V.37, D.38 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manoj Kumar, P. et al., Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate. To be published

Release Date

2015-07-29

Peptides

YagE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

YagE

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