SMTL ID : 9f3j.1

Crystal structure of Kluyveromyces lactis glucokinase in complex with mannose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.1: 18 residues within 4Å: Chain A: S.152, Y.153, P.154, T.169, K.170, N.205, D.206, T.207, I.233, G.237, T.238, N.239, N.271, E.273, G.275, H.304, E.307 Ligands: MLI.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.152, A:T.169, A:K.170, A:N.205, A:N.205, A:T.238, A:T.238, A:N.239, A:E.273 Water bridges: A:G.237, A:G.237, A:H.304 Salt bridges: A:K.170, A:H.304 MAN.8: 17 residues within 4Å: Chain B: S.152, Y.153, P.154, T.169, K.170, N.205, D.206, T.207, I.233, G.237, T.238, N.239, N.271, E.273, G.275, H.304, E.307 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.152, B:T.169, B:K.170, B:N.205, B:N.205, B:T.238, B:N.239, B:E.273, B:E.307 Water bridges: B:G.237, B:G.237, B:H.304 Salt bridges: B:K.170, B:H.304

11 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 9 residues within 4Å: Chain A: G.78, G.79, T.80, N.81, R.83, K.170, G.235, T.236 Ligands: MAN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.78, A:G.79, A:T.80, A:N.81, A:N.81, A:T.236 Water bridges: A:K.170, A:K.170 Salt bridges: A:R.83, A:K.170 MLI.3: 8 residues within 4Å: Chain A: G.312, T.348, E.349, S.352, S.430, V.431, H.434, Y.435 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.348, A:V.431 Hydrogen bonds: A:S.430 MLI.4: 4 residues within 4Å: Chain A: K.23, Q.26, N.282, H.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.26 Salt bridges: A:K.23, A:K.23, A:H.283 MLI.5: 6 residues within 4Å: Chain A: E.244, K.245, N.248, K.411, T.412, N.413 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:K.411 Salt bridges: A:K.245, A:K.411 MLI.6: 7 residues within 4Å: Chain A: R.395, F.399, S.440, M.441, H.444 Chain B: H.420, D.458 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Water bridges: B:H.420, B:H.420, B:R.457 Salt bridges: B:H.420, A:R.395, A:R.395, A:H.444 MLI.7: 6 residues within 4Å: Chain A: H.420 Chain B: R.395, F.399, S.440, M.441, H.444 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:H.420 Salt bridges: A:H.420, B:R.395, B:R.395, B:H.444 MLI.9: 8 residues within 4Å: Chain B: G.78, G.79, T.80, N.81, R.83, K.170, G.235, T.236 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.78, B:G.79, B:T.80, B:N.81, B:N.81, B:T.236 Water bridges: B:R.83, B:R.83, B:K.170, B:K.170 Salt bridges: B:K.170 MLI.10: 5 residues within 4Å: Chain B: I.18, V.19, T.20, S.22, K.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.20, B:T.20 Salt bridges: B:K.23 MLI.11: 4 residues within 4Å: Chain B: Y.30, K.37, N.282, H.283 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.30 Salt bridges: B:H.283, B:H.283 MLI.12: 8 residues within 4Å: Chain B: G.312, T.348, E.349, S.352, S.430, V.431, H.434, Y.435 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.348, B:V.431 Hydrogen bonds: B:S.430, B:S.430 MLI.13: 5 residues within 4Å: Chain B: E.244, K.245, N.248, K.411, T.412 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.248 Salt bridges: B:K.245, B:K.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weisse, R.H. et al., Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1. To be published

Release Date

2025-05-14

Peptides

Glucokinase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucokinase-1

Related Entries With Identical Sequence