SMTL ID : 1m3u.1

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-10-mer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.45, D.84, K.112 Ligands: KPL.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.45, A:D.84, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain B: D.45, D.84, K.112 Ligands: KPL.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.45, B:D.84, H2O.13, H2O.13 MG.5: 4 residues within 4Å: Chain C: D.45, D.84, K.112 Ligands: KPL.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.45, C:D.84, H2O.24, H2O.24 MG.7: 4 residues within 4Å: Chain D: D.45, D.84, K.112 Ligands: KPL.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.45, D:D.84, H2O.36, H2O.36 MG.9: 5 residues within 4Å: Chain E: D.45, S.46, D.84, K.112 Ligands: KPL.10 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.45, E:D.84, H2O.46, H2O.46 MG.11: 4 residues within 4Å: Chain F: D.45, D.84, K.112 Ligands: KPL.12 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.45, F:D.84, H2O.54, H2O.54 MG.13: 4 residues within 4Å: Chain G: D.45, D.84, K.112 Ligands: KPL.14 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.45, G:D.84, H2O.65, H2O.65 MG.15: 4 residues within 4Å: Chain H: D.45, D.84, K.112 Ligands: KPL.16 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.45, H:D.84, H2O.79, H2O.79 MG.17: 5 residues within 4Å: Chain I: D.45, D.84, K.112, E.114 Ligands: KPL.18 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.45, I:D.84, H2O.89, H2O.89 MG.19: 4 residues within 4Å: Chain J: D.45, D.84, K.112 Ligands: KPL.20 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.45, J:D.84, H2O.101, H2O.101

10 x KPL: KETOPANTOATE(Non-covalent)

KPL.2: 13 residues within 4Å: Chain A: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.212, V.214 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.23, A:L.42, A:I.212, A:V.214 Hydrogen bonds: A:S.46, A:S.46, A:K.112, A:E.181 Water bridges: A:G.44, A:H.136 Salt bridges: A:K.112 KPL.4: 13 residues within 4Å: Chain B: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.212, V.214 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.42, B:I.212, B:V.214 Hydrogen bonds: B:S.46, B:K.112, B:E.181 Salt bridges: B:K.112 KPL.6: 14 residues within 4Å: Chain C: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.202, I.212, V.214 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.42, C:I.202, C:I.212, C:V.214 Hydrogen bonds: C:D.45, C:S.46, C:S.46, C:K.112, C:E.181 Water bridges: C:Y.25, C:G.44 Salt bridges: C:K.112 KPL.8: 13 residues within 4Å: Chain D: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.202, V.214 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.202, D:V.214 Hydrogen bonds: D:Y.25, D:D.45, D:S.46, D:S.46, D:K.112, D:E.181 Water bridges: D:G.44, D:E.114, D:E.114 Salt bridges: D:K.112 KPL.10: 12 residues within 4Å: Chain E: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.202 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:T.23, E:I.202 Hydrogen bonds: E:S.46, E:S.46, E:K.112, E:E.181 Water bridges: E:E.114, E:E.114, E:H.136 Salt bridges: E:K.112 KPL.12: 13 residues within 4Å: Chain F: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.202, V.214 Ligands: MG.11 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:T.23, F:I.202, F:I.202, F:V.214 Hydrogen bonds: F:S.46, F:S.46, F:K.112, F:E.181 Water bridges: F:H.136 Salt bridges: F:K.112 KPL.14: 12 residues within 4Å: Chain G: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, V.214 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:T.23, G:L.42, G:V.214 Hydrogen bonds: G:S.46, G:S.46, G:K.112, G:E.181 Water bridges: G:G.44, G:H.136 Salt bridges: G:K.112 KPL.16: 13 residues within 4Å: Chain H: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.202, V.214 Ligands: MG.15 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:T.23, H:I.202, H:V.214 Hydrogen bonds: H:D.45, H:D.45, H:S.46, H:K.112, H:E.181 Water bridges: H:E.114 Salt bridges: H:K.112 KPL.18: 13 residues within 4Å: Chain I: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, P.141, E.181, I.212, V.214 Ligands: MG.17 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:L.42, I:I.212, I:V.214 Hydrogen bonds: I:D.45, I:S.46, I:K.112, I:E.181 Salt bridges: I:K.112 KPL.20: 10 residues within 4Å: Chain J: T.23, L.42, G.44, D.45, S.46, D.84, K.112, H.136, E.181 Ligands: MG.19 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:S.46, J:S.46, J:K.112, J:E.181 Salt bridges: J:K.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

von Delft, F. et al., Structure of E. coli Ketopantoate Hydroxymethyl Transferase Complexed with Ketopantoate and Mg(2+), Solved by Locating 160 Selenomethionine Sites. Structure (2003)

Release Date

2003-07-22

Peptides

3-methyl-2-oxobutanoate hydroxymethyltransferase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

3-methyl-2-oxobutanoate hydroxymethyltransferase