SMTL ID : 2var.1

Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x KDG: 2-KETO-3-DEOXYGLUCONATE(Non-covalent)

KDG.1: 17 residues within 4Å: Chain A: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDF.2, ANP.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.104 Hydrogen bonds: A:G.34, A:S.35, A:S.35, A:N.38, A:Y.106, A:R.166, A:G.255, A:D.294 Water bridges: A:R.108, A:R.108 Salt bridges: A:R.108, A:R.166 KDG.5: 17 residues within 4Å: Chain B: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDF.6, ANP.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.104 Hydrogen bonds: B:G.34, B:S.35, B:N.38, B:Y.106, B:R.166, B:G.255, B:D.258 Water bridges: B:R.108, B:R.108, B:N.164 Salt bridges: B:R.108, B:R.166 KDG.9: 17 residues within 4Å: Chain C: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, L.169, G.255, D.258, D.294 Ligands: KDF.10, ANP.11 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.90, C:L.104 Hydrogen bonds: C:G.34, C:S.35, C:N.38, C:R.166, C:R.166, C:G.255 Salt bridges: C:R.108, C:R.166 KDG.13: 17 residues within 4Å: Chain D: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDF.14, ANP.15 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.104 Hydrogen bonds: D:G.34, D:S.35, D:S.35, D:N.38, D:Y.90, D:R.166, D:G.255, D:D.294 Water bridges: D:R.108, D:R.108 Salt bridges: D:R.108, D:R.166 KDG.17: 17 residues within 4Å: Chain E: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDF.18, ANP.19 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:L.104 Hydrogen bonds: E:G.34, E:S.35, E:N.38, E:R.166, E:G.255, E:D.258 Water bridges: E:R.108, E:R.108, E:N.164 Salt bridges: E:R.108, E:R.166 KDG.21: 17 residues within 4Å: Chain F: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, L.169, G.255, D.258, D.294 Ligands: KDF.22, ANP.23 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.90, F:L.104 Hydrogen bonds: F:G.34, F:S.35, F:N.38, F:Y.106, F:R.166, F:R.166, F:G.255 Salt bridges: F:R.108, F:R.166

6 x KDF: 3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid(Non-covalent)

KDF.2: 17 residues within 4Å: Chain A: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDG.1, ANP.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.11, A:Y.90 Hydrogen bonds: A:G.34, A:S.35, A:N.38, A:Y.106, A:R.166, A:D.294 Water bridges: A:R.108, A:R.108 Salt bridges: A:R.108, A:R.166 KDF.6: 17 residues within 4Å: Chain B: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDG.5, ANP.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.11, B:Y.90 Hydrogen bonds: B:G.34, B:S.35, B:N.38, B:Y.106, B:R.166 Water bridges: B:R.108, B:R.108 Salt bridges: B:R.108, B:R.166 KDF.10: 16 residues within 4Å: Chain C: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, G.255, D.258, D.294 Ligands: KDG.9, ANP.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.11, C:Y.90 Hydrogen bonds: C:G.34, C:S.35, C:N.38, C:R.166 Salt bridges: C:R.108, C:R.166 KDF.14: 17 residues within 4Å: Chain D: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDG.13, ANP.15 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.11, D:Y.90 Hydrogen bonds: D:G.34, D:S.35, D:N.38, D:Y.90, D:R.166, D:D.294 Water bridges: D:R.108, D:R.108 Salt bridges: D:R.108, D:R.166 KDF.18: 17 residues within 4Å: Chain E: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, T.254, G.255, D.258, D.294 Ligands: KDG.17, ANP.19 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.11, E:Y.90 Hydrogen bonds: E:G.34, E:S.35, E:N.38, E:R.166 Water bridges: E:R.108, E:R.108 Salt bridges: E:R.108, E:R.166 KDF.22: 16 residues within 4Å: Chain F: L.11, A.33, G.34, S.35, N.38, Y.90, L.104, Y.106, R.108, I.137, R.166, G.255, D.258, D.294 Ligands: KDG.21, ANP.23 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:L.11, F:Y.90 Hydrogen bonds: F:G.34, F:S.35, F:N.38, F:Y.106, F:R.166 Salt bridges: F:R.108, F:R.166

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 22 residues within 4Å: Chain A: N.164, R.166, K.226, G.228, S.229, G.231, A.232, A.245, Y.246, V.250, T.254, G.255, A.256, G.257, D.258, M.260, I.282, S.285, I.289 Ligands: KDG.1, KDF.2, AMP.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.164, A:R.166, A:K.226, A:G.228, A:G.255, A:A.256, A:G.257, A:D.258, A:S.285 Water bridges: A:N.164, A:N.164, A:Y.246 Salt bridges: A:K.226 ANP.7: 23 residues within 4Å: Chain B: N.164, R.166, K.226, G.228, S.229, G.231, A.232, A.245, Y.246, V.250, P.253, T.254, G.255, A.256, G.257, D.258, M.260, I.282, S.285, I.289 Ligands: KDG.5, KDF.6, AMP.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.166, B:R.166, B:K.226, B:G.228, B:G.255, B:G.257, B:D.258, B:S.285 Water bridges: B:K.101, B:N.164, B:N.164, B:N.164, B:Y.246 Salt bridges: B:K.226 ANP.11: 21 residues within 4Å: Chain C: N.164, R.166, K.226, G.228, S.229, G.231, A.245, Y.246, V.250, T.254, G.255, A.256, G.257, D.258, M.260, I.282, S.285, I.289 Ligands: KDG.9, KDF.10, AMP.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:N.164, C:R.166, C:G.228, C:P.253, C:G.255, C:A.256, C:G.257, C:D.258, C:D.258, C:S.285 Water bridges: C:K.101, C:K.101 Salt bridges: C:K.226 ANP.15: 22 residues within 4Å: Chain D: N.164, R.166, K.226, G.228, S.229, G.231, A.232, A.245, Y.246, V.250, T.254, G.255, A.256, G.257, D.258, M.260, I.282, S.285, I.289 Ligands: KDG.13, KDF.14, AMP.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:N.164, D:R.166, D:K.226, D:G.228, D:G.255, D:A.256, D:G.257, D:D.258, D:S.285 Water bridges: D:K.101, D:N.164, D:N.164 Salt bridges: D:K.226 ANP.19: 23 residues within 4Å: Chain E: N.164, R.166, K.226, G.228, S.229, G.231, A.232, A.245, Y.246, V.250, P.253, T.254, G.255, A.256, G.257, D.258, M.260, I.282, S.285, I.289 Ligands: KDG.17, KDF.18, AMP.20 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:R.166, E:R.166, E:K.226, E:G.228, E:G.255, E:G.257, E:D.258, E:S.285 Water bridges: E:K.101, E:N.164, E:N.164, E:N.164, E:D.195, E:Y.246 Salt bridges: E:K.226 ANP.23: 21 residues within 4Å: Chain F: N.164, R.166, K.226, G.228, S.229, G.231, A.245, Y.246, V.250, T.254, G.255, A.256, G.257, D.258, M.260, I.282, S.285, I.289 Ligands: KDG.21, KDF.22, AMP.24 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:N.164, F:R.166, F:G.228, F:P.253, F:G.255, F:A.256, F:G.257, F:D.258, F:D.258, F:S.285 Water bridges: F:K.101, F:K.101 Salt bridges: F:K.226

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 15 residues within 4Å: Chain A: K.226, L.227, G.228, S.229, G.231, A.232, A.245, Y.246, V.250, A.256, M.260, I.282, S.285, I.289 Ligands: ANP.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.227, A:G.228, A:S.285 Water bridges: A:Y.246 Salt bridges: A:K.226 AMP.8: 14 residues within 4Å: Chain B: K.226, G.228, S.229, G.231, A.245, Y.246, V.250, A.256, G.257, M.260, I.282, S.285, I.289 Ligands: ANP.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.228, B:G.257, B:S.285 Salt bridges: B:K.226 AMP.12: 12 residues within 4Å: Chain C: K.226, G.228, S.229, G.231, A.245, Y.246, A.256, M.260, I.282, S.285, I.289 Ligands: ANP.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.228, C:S.285 Salt bridges: C:K.226 AMP.16: 15 residues within 4Å: Chain D: K.226, L.227, G.228, S.229, G.231, A.232, A.245, Y.246, V.250, A.256, M.260, I.282, S.285, I.289 Ligands: ANP.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.227, D:G.228, D:S.285 Salt bridges: D:K.226 AMP.20: 14 residues within 4Å: Chain E: K.226, G.228, S.229, G.231, A.245, Y.246, V.250, A.256, G.257, M.260, I.282, S.285, I.289 Ligands: ANP.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.228, E:G.257, E:S.285 Water bridges: E:D.195, E:D.195 Salt bridges: E:K.226 AMP.24: 12 residues within 4Å: Chain F: K.226, G.228, S.229, G.231, A.245, Y.246, A.256, M.260, I.282, S.285, I.289 Ligands: ANP.23 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.228, F:S.285 Salt bridges: F:K.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Potter, J.A. et al., The Structure of Sulfolobus Solfataricus 2-Keto-3-Deoxygluconate Kinase. Acta Crystallogr.,Sect.D (2008)

Release Date

2007-10-02

Peptides

FRUCTOKINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

FRUCTOKINASE

Related Entries With Identical Sequence