SMTL ID : 6gv2.1

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F,A198F variant in complex with L-2-keto, 3-deoxy-galactonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x SSH: 3-DEOXY-D-ARABINO-HEXONIC ACID(Post Translational Modification)

SSH.1: 14 residues within 4Å: Chain A: P.7, F.39, G.42, T.43, T.44, F.130, Y.132, K.155, T.157, G.179, V.196, F.198, L.242 Ligands: GXV.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.7, A:F.130, A:K.155 Hydrogen bonds: A:T.43, A:T.43, A:T.44, A:T.44, A:Y.132, A:T.157, A:G.179 Salt bridges: A:K.155 SSH.7: 15 residues within 4Å: Chain B: P.7, F.39, G.42, T.43, T.44, F.130, Y.132, K.155, T.157, G.179, V.196, F.198, L.242, N.245 Ligands: GXV.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.130 Hydrogen bonds: B:T.43, B:T.43, B:T.44, B:T.44, B:T.44, B:T.157 Salt bridges: B:K.155 SSH.14: 14 residues within 4Å: Chain C: P.7, F.39, G.42, T.43, T.44, F.130, Y.132, K.155, T.157, G.179, V.196, F.198, L.242 Ligands: GXV.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:P.7, C:F.130, C:K.155 Hydrogen bonds: C:T.43, C:T.43, C:T.44, C:T.44, C:Y.132, C:T.157, C:G.179 Salt bridges: C:K.155 SSH.20: 15 residues within 4Å: Chain D: P.7, F.39, G.42, T.43, T.44, F.130, Y.132, K.155, T.157, G.179, V.196, F.198, L.242, N.245 Ligands: GXV.21 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.130 Hydrogen bonds: D:T.43, D:T.43, D:T.44, D:T.44, D:T.44, D:K.155, D:T.157 Salt bridges: D:K.155

4 x GXV: L-glyceraldehyde(Non-covalent)

GXV.2: 9 residues within 4Å: Chain A: T.43, T.44, Y.132, T.157, F.198, S.241, L.242, N.245 Ligands: SSH.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.132, A:N.245 Water bridges: A:S.241, D:R.106 GXV.8: 9 residues within 4Å: Chain B: T.43, T.44, Y.132, T.157, F.198, S.241, L.242, N.245 Ligands: SSH.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.241, B:S.241, B:N.245 GXV.15: 9 residues within 4Å: Chain C: T.43, T.44, Y.132, T.157, F.198, S.241, L.242, N.245 Ligands: SSH.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.132, C:N.245 Water bridges: C:S.241, B:R.106 GXV.21: 9 residues within 4Å: Chain D: T.43, T.44, Y.132, T.157, F.198, S.241, L.242, N.245 Ligands: SSH.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.241, D:S.241, D:N.245

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

EDO.3: 4 residues within 4Å: Chain A: K.114, K.117, T.118, E.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.114, A:E.121 EDO.9: 11 residues within 4Å: Chain B: G.240, S.241, L.242, S.243, I.264 Chain C: Y.104, P.105, R.106, M.107, S.108, H.111 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.241, B:L.242, B:S.243, B:S.243, C:R.106 EDO.16: 4 residues within 4Å: Chain C: K.114, K.117, T.118, E.121 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.114, C:E.121 EDO.22: 11 residues within 4Å: Chain A: Y.104, P.105, R.106, M.107, S.108, H.111 Chain D: G.240, S.241, L.242, S.243, I.264 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.241, D:L.242, D:S.243, D:S.243, A:R.106

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 13 residues within 4Å: Chain A: F.239, G.240, S.241, L.242, S.243, P.263, I.264, F.265 Chain D: P.105, R.106, M.107, S.108, H.111 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.240, A:S.241, A:L.242, A:S.243, D:P.105, D:S.108, D:S.108 GOL.5: 6 residues within 4Å: Chain A: C.120, S.123, H.125, P.126, V.127, C.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.120, A:C.120, A:C.150 Water bridges: A:S.123 GOL.6: 4 residues within 4Å: Chain A: E.121, V.122, S.123, P.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.121, A:V.122 Water bridges: A:S.123 GOL.10: 5 residues within 4Å: Chain B: N.171, P.172, N.173, M.174 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.173, B:N.173, B:M.174 Water bridges: B:N.171 GOL.11: 6 residues within 4Å: Chain B: G.149, C.150, F.151, T.152 Ligands: GOL.10, GOL.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.152 GOL.12: 4 residues within 4Å: Chain B: K.60, Y.63, D.90, F.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.90 GOL.13: 8 residues within 4Å: Chain B: C.120, S.123, H.125, P.126, V.127, C.150, T.152 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.125 Water bridges: B:C.120, B:S.123, B:H.125, B:T.152 GOL.17: 13 residues within 4Å: Chain B: P.105, R.106, M.107, S.108, H.111 Chain C: F.239, G.240, S.241, L.242, S.243, P.263, I.264, F.265 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:G.240, C:S.241, C:L.242, C:S.243, B:P.105, B:S.108, B:S.108 GOL.18: 6 residues within 4Å: Chain C: C.120, S.123, H.125, P.126, V.127, C.150 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:C.120, C:C.120, C:C.150 Water bridges: C:S.123 GOL.19: 4 residues within 4Å: Chain C: E.121, V.122, S.123, P.124 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.121, C:V.122 Water bridges: C:S.123 GOL.23: 5 residues within 4Å: Chain D: N.171, P.172, N.173, M.174 Ligands: GOL.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.173, D:N.173, D:M.174 Water bridges: D:N.171 GOL.24: 6 residues within 4Å: Chain D: G.149, C.150, F.151, T.152 Ligands: GOL.23, GOL.26 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.152 GOL.25: 4 residues within 4Å: Chain D: K.60, Y.63, D.90, F.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.90 GOL.26: 8 residues within 4Å: Chain D: C.120, S.123, H.125, P.126, V.127, C.150, T.152 Ligands: GOL.24 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:C.120, D:S.123, D:H.125, D:T.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crennell, S.J. et al., Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant. To Be Published

Release Date

2019-07-03

Peptides

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

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