SMTL ID : 6h2s.1

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant, pyruvate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 9 residues within 4Å: Chain A: P.6, F.38, T.42, T.43, Y.129, V.156, G.178, V.195, L.197 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.156 Hydrogen bonds: A:T.42, A:T.43, A:T.43, A:Y.129 PYR.6: 9 residues within 4Å: Chain B: P.6, F.38, T.42, T.43, Y.129, V.156, G.178, V.195, L.197 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.156, B:V.195 Hydrogen bonds: B:T.42, B:T.43, B:Y.129 Water bridges: B:T.43, B:T.43 PYR.9: 10 residues within 4Å: Chain C: P.6, F.38, G.41, T.42, T.43, Y.129, V.156, G.178, V.195, L.197 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.6, C:V.156, C:V.195 Hydrogen bonds: C:T.42, C:T.42, C:T.43, C:Y.129, C:Y.129 PYR.12: 9 residues within 4Å: Chain D: P.6, F.38, T.42, T.43, Y.129, V.156, G.178, V.195, L.197 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.156, D:V.195 Hydrogen bonds: D:T.42, D:T.43, D:Y.129 Water bridges: D:V.195, D:L.197

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 13 residues within 4Å: Chain A: F.238, G.239, S.240, L.241, S.242, P.262, I.263, F.264 Chain B: P.104, R.105, M.106, S.107, H.110 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.107, B:S.107, B:S.107, A:S.240, A:S.240, A:S.240, A:L.241, A:S.242 GOL.3: 6 residues within 4Å: Chain A: K.36, N.66, K.67, D.91, I.92, V.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.67, A:D.91 GOL.7: 12 residues within 4Å: Chain A: Y.103, P.104, R.105, M.106, S.107, H.110 Chain B: F.238, G.239, S.240, L.241, S.242, I.263 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.107, A:H.110, B:S.240, B:L.241, B:S.242, B:S.242 Water bridges: A:P.104 GOL.8: 6 residues within 4Å: Chain B: L.111, G.136, K.137, D.138, I.139, V.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.136, B:D.138, B:D.138 GOL.10: 12 residues within 4Å: Chain C: F.238, G.239, S.240, L.241, S.242, I.263, F.264 Chain D: P.104, R.105, M.106, S.107, H.110 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.240, C:L.241, C:S.242, C:S.242, D:S.107, D:S.107, D:S.107 Water bridges: D:P.104 GOL.13: 14 residues within 4Å: Chain C: Y.103, P.104, R.105, M.106, S.107, H.110 Chain D: F.238, G.239, S.240, L.241, S.242, P.262, I.263, F.264 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.240, D:L.241, D:S.242, C:R.105, C:S.107, C:S.107 GOL.14: 5 residues within 4Å: Chain D: Y.62, D.63, V.64, T.65, N.66 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.64, D:N.66

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 13 residues within 4Å: Chain A: Y.102, Y.103, P.104, P.132, T.133, A.134, T.135, G.136, K.137 Chain B: T.133, A.134, T.135, G.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.103, A:T.133, A:G.136, A:K.137 PEG.11: 11 residues within 4Å: Chain C: Y.102, Y.103, P.104, P.132, T.133, T.135, G.136, K.137 Chain D: T.133, A.134, G.136 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.133, C:G.136, C:G.136, C:K.137 Water bridges: D:Y.102

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 6 residues within 4Å: Chain A: C.119, S.122, H.124, P.125, V.126, C.149 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crennell, S.J. et al., Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant. To Be Published

Release Date

2019-07-31

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
C

D
D

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

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