SMTL ID : 2dcn.2 (1 other biounit)

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate (alpha-furanose form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-hexamer

Ligands

23 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: N.164 Ligands: CKP.8, ADP.9 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: D.130 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: H.78, Y.125 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: N.164, R.166 Ligands: CKP.14, ADP.15 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain C: N.164, R.166, K.224 Ligands: CKP.20, ADP.21 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: ADP.21 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain C: V.76 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain D: N.164, R.166, K.224 Ligands: CKP.27, ADP.28 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Ligands: ADP.28 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain D: M.79 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain D: Y.125 No protein-ligand interaction detected (PLIP) MG.29: 5 residues within 4Å: Chain E: N.164, R.166, K.224 Ligands: CKP.33, ADP.34 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Ligands: ADP.34 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain F: N.164, R.166 Ligands: CKP.40, ADP.41 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Ligands: ADP.41 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain F: V.76 No protein-ligand interaction detected (PLIP)

6 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: D.250, T.252, N.286, I.289, G.291 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.250, A:T.252, A:N.286, A:I.289, H2O.1 K.13: 5 residues within 4Å: Chain B: D.250, T.252, N.286, I.289, G.291 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.250, B:T.252, B:N.286, B:I.289 K.19: 5 residues within 4Å: Chain C: D.250, T.252, N.286, I.289, G.291 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.250, C:T.252, C:N.286, C:I.289 K.26: 5 residues within 4Å: Chain D: D.250, T.252, N.286, I.289, G.291 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.250, D:T.252, D:N.286, D:I.289, H2O.20 K.32: 5 residues within 4Å: Chain E: D.250, T.252, N.286, I.289, G.291 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.250, E:T.252, E:N.286, E:I.289 K.39: 5 residues within 4Å: Chain F: D.250, T.252, N.286, I.289, G.291 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.250, F:T.252, F:N.286, F:I.289, H2O.32

6 x CKP: 6-O-phosphono-beta-D-psicofuranosonic acid(Non-covalent)

CKP.8: 19 residues within 4Å: Chain A: L.11, A.33, G.34, S.35, N.38, F.90, Y.106, R.108, I.137, N.164, R.166, T.252, G.253, A.254, G.255, D.256, D.292 Ligands: MG.1, ADP.9 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.34, A:S.35, A:N.38, A:Y.106, A:R.166, A:G.253, A:G.255, A:D.256, A:D.292 Water bridges: A:S.104, A:Y.106, A:R.108, A:R.108, A:N.164, A:N.164, A:R.166, A:A.254, A:A.254 Salt bridges: A:R.108, A:R.166, A:R.166 CKP.14: 19 residues within 4Å: Chain B: L.11, A.33, G.34, S.35, N.38, F.90, Y.106, R.108, I.137, N.164, R.166, T.252, G.253, A.254, G.255, D.256, D.292 Ligands: MG.11, ADP.15 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.34, B:S.35, B:N.38, B:R.166, B:G.253, B:G.255, B:D.256, B:D.292 Water bridges: B:S.104, B:Y.106, B:R.108, B:R.108, B:N.164, B:N.164 Salt bridges: B:R.108, B:R.166, B:R.166 CKP.20: 19 residues within 4Å: Chain C: L.11, A.33, G.34, S.35, N.38, F.90, Y.106, R.108, I.137, N.164, R.166, T.252, G.253, A.254, G.255, D.256, D.292 Ligands: MG.16, ADP.21 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.34, C:S.35, C:N.38, C:Y.106, C:R.166, C:G.255, C:D.256, C:D.292 Water bridges: C:S.104, C:Y.106, C:R.108, C:R.108, C:N.164, C:R.166, C:A.254, C:A.254 Salt bridges: C:R.108, C:R.166, C:R.166 CKP.27: 19 residues within 4Å: Chain D: L.11, A.33, G.34, S.35, N.38, F.90, Y.106, R.108, I.137, N.164, R.166, T.252, G.253, A.254, G.255, D.256, D.292 Ligands: MG.22, ADP.28 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:G.34, D:S.35, D:N.38, D:R.166, D:G.253, D:G.255, D:D.256, D:D.292 Water bridges: D:S.104, D:S.104, D:R.108, D:R.108, D:N.164, D:N.164, D:A.254, D:A.254 Salt bridges: D:R.108, D:R.166, D:R.166 CKP.33: 19 residues within 4Å: Chain E: L.11, A.33, G.34, S.35, N.38, F.90, Y.106, R.108, I.137, N.164, R.166, T.252, G.253, A.254, G.255, D.256, D.292 Ligands: MG.29, ADP.34 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:G.34, E:S.35, E:N.38, E:R.166, E:G.253, E:G.255, E:D.256, E:D.292 Water bridges: E:S.104, E:Y.106, E:R.108, E:R.108, E:N.164, E:R.166, E:D.256 Salt bridges: E:R.108, E:R.166, E:R.166 CKP.40: 19 residues within 4Å: Chain F: L.11, A.33, G.34, S.35, N.38, F.90, Y.106, R.108, I.137, N.164, R.166, T.252, G.253, A.254, G.255, D.256, D.292 Ligands: MG.36, ADP.41 21 PLIP interactions: 21 interactions with chain F Hydrogen bonds: F:G.34, F:S.35, F:N.38, F:Y.106, F:R.166, F:G.253, F:G.255, F:D.256, F:D.292 Water bridges: F:S.104, F:S.104, F:R.108, F:R.108, F:N.164, F:N.164, F:R.166, F:A.254, F:A.254 Salt bridges: F:R.108, F:R.166, F:R.166

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.9: 18 residues within 4Å: Chain A: D.194, K.224, G.226, P.227, G.229, Y.244, V.246, V.248, V.251, A.254, G.255, L.258, I.280, S.283, V.287 Ligands: MG.1, MG.2, CKP.8 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.194, A:G.226, A:G.255 Water bridges: A:N.164, A:R.166, A:K.224, A:K.224 Salt bridges: A:K.224, A:K.224 ADP.15: 19 residues within 4Å: Chain B: D.194, K.224, L.225, G.226, P.227, G.229, Y.244, V.246, V.248, V.251, A.254, G.255, L.258, I.280, S.283, V.287 Ligands: MG.11, MG.12, CKP.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.194, B:G.226, B:G.229, B:G.255 Water bridges: B:R.166, B:K.224, B:K.224, B:V.246 Salt bridges: B:K.224, B:K.224 ADP.21: 19 residues within 4Å: Chain C: D.194, K.224, L.225, G.226, P.227, G.229, Y.244, V.246, V.248, V.251, A.254, G.255, L.258, I.280, S.283, V.287 Ligands: MG.16, MG.17, CKP.20 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.194, C:D.194, C:G.226, C:G.229, C:G.255 Water bridges: C:K.224, C:K.224, C:K.224 Salt bridges: C:K.224 ADP.28: 18 residues within 4Å: Chain D: D.194, K.224, L.225, G.226, P.227, G.229, Y.244, V.248, V.251, A.254, G.255, L.258, I.280, S.283, V.287 Ligands: MG.22, MG.23, CKP.27 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.194, D:D.194, D:G.226, D:G.229 Water bridges: D:K.101, D:K.101, D:K.224, D:K.224, D:G.255, D:G.255 Salt bridges: D:K.224, D:K.224 ADP.34: 18 residues within 4Å: Chain E: D.194, K.224, L.225, G.226, P.227, G.229, Y.244, V.248, V.251, A.254, G.255, L.258, I.280, S.283, V.287 Ligands: MG.29, MG.30, CKP.33 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:D.194, E:D.194, E:G.226, E:G.229, E:G.229, E:T.284 Water bridges: E:K.101, E:K.101, E:N.164, E:N.164, E:D.194, E:K.224, E:K.224, E:G.255, E:G.255 Salt bridges: E:K.224 ADP.41: 18 residues within 4Å: Chain F: D.194, K.224, L.225, G.226, P.227, G.229, Y.244, V.248, V.251, A.254, G.255, L.258, I.280, S.283, V.287 Ligands: MG.36, MG.37, CKP.40 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.194, F:G.226, F:G.229, F:G.255 Water bridges: F:K.101, F:N.164, F:K.224, F:K.224, F:Y.244 Salt bridges: F:K.224, F:K.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okazaki, S. et al., Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate. To be Published

Release Date

2006-01-31

Peptides

hypothetical fructokinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

hypothetical fructokinase

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