SMTL ID : 8upp.1

Campylobacter jejuni ketol-acid reductoisomerase in complex with NADPH and Hoe704

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-12-mer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.192, E.196 Ligands: MG.2, X9W.45 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:E.196, H2O.2, H2O.59 MG.2: 4 residues within 4Å: Chain A: K.132, D.192 Ligands: MG.1, X9W.45 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.192, H2O.3, H2O.58, H2O.59 MG.5: 4 residues within 4Å: Chain B: D.192, E.196 Ligands: MG.6, X9W.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.192, B:E.196, H2O.7, H2O.8 MG.6: 5 residues within 4Å: Chain B: K.132, D.192, E.196 Ligands: MG.5, X9W.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.192, H2O.8, H2O.8, H2O.13 MG.10: 4 residues within 4Å: Chain C: D.192, E.196 Ligands: X9W.9, MG.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.192, C:E.196, H2O.8, H2O.14 MG.11: 4 residues within 4Å: Chain C: K.132, D.192 Ligands: X9W.9, MG.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.192, H2O.9, H2O.9, H2O.12 MG.13: 4 residues within 4Å: Chain D: D.192, E.196 Ligands: MG.14, X9W.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.192, D:E.196, H2O.18, H2O.18 MG.14: 4 residues within 4Å: Chain D: D.192 Chain G: E.228 Ligands: MG.13, X9W.15 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.192, H2O.18, H2O.32, H2O.34 MG.17: 4 residues within 4Å: Chain E: D.192, E.196 Ligands: MG.18, X9W.29 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.192, E:E.196, H2O.24, H2O.39 MG.18: 3 residues within 4Å: Chain E: D.192 Ligands: MG.17, X9W.29 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.192, H2O.23, H2O.38, H2O.38 MG.21: 4 residues within 4Å: Chain F: D.192, E.196 Ligands: MG.22, X9W.41 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.192, F:E.196, H2O.54, H2O.54 MG.22: 4 residues within 4Å: Chain F: D.192, E.196 Ligands: MG.21, X9W.41 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.192, H2O.28, H2O.28, H2O.53 MG.25: 4 residues within 4Å: Chain G: D.192, E.196 Ligands: MG.26, X9W.27 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.192, G:E.196, H2O.33, H2O.33 MG.26: 5 residues within 4Å: Chain D: E.228 Chain G: D.192, E.196 Ligands: MG.25, X9W.27 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.192, H2O.17, H2O.18, H2O.32 MG.30: 5 residues within 4Å: Chain H: H.109, D.192, E.196 Ligands: X9W.20, MG.31 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.192, H:E.196, H2O.23, H2O.40 MG.31: 3 residues within 4Å: Chain H: D.192 Ligands: X9W.20, MG.30 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.192, H2O.23, H2O.39, H2O.39 MG.33: 4 residues within 4Å: Chain I: D.192, E.196 Ligands: MG.34, X9W.37 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:D.192, I:E.196, H2O.44, H2O.48 MG.34: 5 residues within 4Å: Chain I: D.192, E.196 Chain J: E.228 Ligands: MG.33, X9W.37 4 PLIP interactions: 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:D.192, H2O.43, H2O.48, H2O.48 MG.38: 4 residues within 4Å: Chain J: D.192, E.196 Ligands: X9W.36, MG.39 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.192, J:E.196, H2O.43, H2O.49 MG.39: 5 residues within 4Å: Chain I: E.228, E.232 Chain J: D.192 Ligands: X9W.36, MG.38 4 PLIP interactions: 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:D.192, H2O.43, H2O.43, H2O.48 MG.42: 4 residues within 4Å: Chain K: D.192, E.196 Ligands: X9W.24, MG.43 4 PLIP interactions: 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.192, K:E.196, H2O.28, H2O.54 MG.43: 4 residues within 4Å: Chain F: E.232 Chain K: D.192 Ligands: X9W.24, MG.42 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:D.192, H2O.27, H2O.53, H2O.54 MG.46: 4 residues within 4Å: Chain L: D.192, E.196 Ligands: X9W.4, MG.47 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.192, L:E.196, H2O.3, H2O.60 MG.47: 3 residues within 4Å: Chain L: D.192 Ligands: X9W.4, MG.46 4 PLIP interactions: 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:D.192, H2O.2, H2O.3, H2O.60

12 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.3: 26 residues within 4Å: Chain A: G.25, F.26, G.27, S.28, Q.29, G.30, L.48, R.49, S.52, S.54, L.81, A.82, P.83, D.84, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Chain L: S.251, I.252, S.253 Ligands: X9W.45 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain L Hydrogen bonds: A:F.26, A:F.26, A:S.28, A:S.28, A:Q.29, A:Q.29, A:G.30, A:R.49, A:R.49, A:S.54, A:A.82, A:D.84, A:Q.87, A:G.135, L:I.252, L:S.253 Water bridges: A:S.28, A:H.109, A:H.109, L:I.252 NDP.8: 26 residues within 4Å: Chain B: G.25, F.26, G.27, S.28, Q.29, G.30, L.48, R.49, S.52, S.54, L.81, A.82, P.83, D.84, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Chain C: S.251, I.252, S.253 Ligands: X9W.7 23 PLIP interactions: 19 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:F.26, B:F.26, B:S.28, B:S.28, B:S.28, B:Q.29, B:G.30, B:R.49, B:R.49, B:R.49, B:S.54, B:S.54, B:A.82, B:D.84, B:Q.87, B:G.135, C:I.252, C:S.253, C:S.253 Water bridges: B:G.27, B:G.27, B:H.109, C:N.254 NDP.12: 27 residues within 4Å: Chain B: S.251, I.252, S.253 Chain C: G.25, F.26, G.27, S.28, Q.29, L.48, R.49, S.52, V.53, S.54, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Ligands: X9W.9 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:F.26, C:S.28, C:S.28, C:S.28, C:Q.29, C:R.49, C:V.53, C:S.54, C:S.54, C:D.84, C:Q.87, C:G.135, B:S.251 Water bridges: C:G.27, C:G.30, C:R.49, C:R.49, C:H.109, C:H.109, B:N.254 NDP.16: 28 residues within 4Å: Chain D: G.25, F.26, G.27, S.28, Q.29, G.47, L.48, R.49, S.52, S.54, V.68, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Chain G: S.251, I.252, S.253 Ligands: X9W.15 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain G Hydrophobic interactions: D:Q.29 Hydrogen bonds: D:F.26, D:F.26, D:S.28, D:S.28, D:Q.29, D:Q.29, D:R.49, D:S.54, D:S.54, D:S.54, D:D.84, D:Q.87, D:G.135, G:S.251 Water bridges: D:G.27, D:S.28, D:H.109, D:H.109, G:I.252, G:N.254 NDP.19: 26 residues within 4Å: Chain E: I.24, G.25, F.26, G.27, S.28, Q.29, G.47, R.49, S.52, S.54, L.81, A.82, P.83, D.84, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Chain H: S.251, I.252, S.253 Ligands: X9W.29 21 PLIP interactions: 19 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: E:Q.29 Hydrogen bonds: E:F.26, E:F.26, E:S.28, E:S.28, E:S.28, E:Q.29, E:Q.29, E:R.49, E:S.52, E:S.54, E:S.54, E:A.82, E:D.84, E:Q.87, E:G.135, H:S.251 Water bridges: E:G.27, E:G.30, E:H.109, H:N.254 NDP.23: 26 residues within 4Å: Chain F: G.25, F.26, G.27, S.28, Q.29, R.49, S.52, V.53, S.54, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Chain K: S.251, I.252, S.253 Ligands: X9W.41 23 PLIP interactions: 19 interactions with chain F, 4 interactions with chain K Hydrogen bonds: F:G.25, F:F.26, F:F.26, F:S.28, F:S.28, F:S.28, F:Q.29, F:R.49, F:V.53, F:S.54, F:S.54, F:S.54, F:D.84, F:Q.87, F:G.135, K:S.253, K:S.253 Water bridges: F:G.27, F:G.30, F:Q.87, F:H.109, K:N.254, K:N.254 NDP.28: 28 residues within 4Å: Chain D: S.251, I.252, S.253 Chain G: G.25, F.26, G.27, S.28, Q.29, G.47, L.48, R.49, S.52, S.54, V.68, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Ligands: X9W.27 20 PLIP interactions: 19 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:Q.29 Hydrogen bonds: G:F.26, G:F.26, G:S.28, G:S.28, G:Q.29, G:Q.29, G:R.49, G:S.54, G:S.54, G:D.84, G:Q.87, G:G.135, D:S.251 Water bridges: G:G.27, G:S.28, G:G.30, G:V.53, G:I.80, G:H.109 NDP.32: 26 residues within 4Å: Chain E: S.251, I.252, S.253 Chain H: G.25, F.26, G.27, S.28, Q.29, R.49, S.52, S.54, V.68, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Ligands: X9W.20 19 PLIP interactions: 15 interactions with chain H, 4 interactions with chain E Hydrophobic interactions: H:Q.29 Hydrogen bonds: H:F.26, H:G.27, H:S.28, H:Q.29, H:R.49, H:V.53, H:S.54, H:D.84, H:Q.87, H:G.135, E:I.252, E:S.253 Water bridges: H:G.30, H:R.49, H:Q.87, H:H.109, E:N.254, E:N.254 NDP.35: 26 residues within 4Å: Chain I: G.25, F.26, G.27, S.28, Q.29, L.48, S.52, V.53, S.54, V.68, L.81, A.82, P.83, D.84, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Chain J: S.251, I.252, S.253 Ligands: X9W.37 17 PLIP interactions: 15 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:G.25, I:F.26, I:F.26, I:S.28, I:Q.29, I:G.30, I:S.54, I:S.54, I:S.54, I:D.84, I:Q.87, I:G.135, J:I.252 Water bridges: I:G.27, I:S.28, I:S.28, J:N.254 NDP.40: 27 residues within 4Å: Chain I: S.251, I.252, S.253 Chain J: G.25, F.26, G.27, S.28, Q.29, L.48, R.49, S.52, V.53, S.54, V.68, L.81, A.82, P.83, D.84, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Ligands: X9W.36 19 PLIP interactions: 18 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:F.26, J:F.26, J:S.28, J:S.28, J:S.28, J:Q.29, J:Q.29, J:G.30, J:R.49, J:S.54, J:S.54, J:S.54, J:D.84, J:Q.87, J:G.135, I:S.251 Water bridges: J:G.27, J:G.27 Salt bridges: J:R.49 NDP.44: 24 residues within 4Å: Chain F: S.251, I.252, S.253 Chain K: F.26, G.27, S.28, Q.29, R.49, S.52, S.54, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Ligands: X9W.24 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain F Hydrophobic interactions: K:Q.29 Hydrogen bonds: K:F.26, K:F.26, K:S.28, K:S.28, K:S.28, K:Q.29, K:Q.29, K:S.54, K:D.84, K:Q.87, K:G.135, F:S.253 Water bridges: K:G.27, K:G.30, K:I.80, K:H.109, F:N.254 NDP.48: 25 residues within 4Å: Chain A: S.251, I.252, S.253 Chain L: F.26, G.27, S.28, Q.29, R.49, S.52, V.53, S.54, L.81, A.82, P.83, D.84, I.86, Q.87, I.90, A.108, H.109, P.131, A.133, P.134, G.135 Ligands: X9W.4 24 PLIP interactions: 21 interactions with chain L, 3 interactions with chain A Hydrophobic interactions: L:Q.29 Hydrogen bonds: L:F.26, L:F.26, L:G.27, L:S.28, L:S.28, L:S.28, L:Q.29, L:R.49, L:R.49, L:V.53, L:S.54, L:S.54, L:D.84, L:Q.87, L:G.135, A:S.251, A:S.253 Water bridges: L:G.30, L:R.49, L:R.49, L:I.80, L:H.109, A:N.254

12 x X9W: (2R)-(dimethylphosphoryl)(hydroxy)acetic acid

X9W.4: 14 residues within 4Å: Chain A: E.232, I.236, I.252, S.253, A.256 Chain L: A.133, P.134, D.192, E.196, L.200, C.201 Ligands: MG.46, MG.47, NDP.48 6 PLIP interactions: 4 interactions with chain L, 2 interactions with chain A Hydrogen bonds: L:E.196, L:E.196, A:S.253 Water bridges: L:K.132, L:D.192, A:S.253 X9W.7: 14 residues within 4Å: Chain B: A.133, P.134, D.192, E.196, L.200, C.201 Chain C: E.232, I.236, I.252, S.253, A.256 Ligands: MG.5, MG.6, NDP.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.133, B:E.196, C:S.253 Water bridges: B:K.132, B:K.132 X9W.9: 14 residues within 4Å: Chain B: E.232, I.236, I.252, S.253, A.256 Chain C: A.133, P.134, D.192, E.196, L.200, C.201 Ligands: MG.10, MG.11, NDP.12 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:D.192, C:E.196, B:S.253, B:A.256 Water bridges: C:K.132, C:E.196, C:E.196, B:S.253, B:S.253 X9W.15: 13 residues within 4Å: Chain D: A.133, P.134, D.192, E.196, C.201 Chain G: E.232, I.236, I.252, S.253, A.256 Ligands: MG.13, MG.14, NDP.16 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain G Hydrogen bonds: D:A.133, D:E.196, G:S.253 Water bridges: D:H.109, D:K.132, D:E.196, D:E.196, G:S.253, G:A.256 X9W.20: 13 residues within 4Å: Chain E: E.232, I.236, I.252, S.253, A.256 Chain H: A.133, P.134, D.192, E.196, C.201 Ligands: MG.30, MG.31, NDP.32 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:A.133, H:E.196, E:S.253 Water bridges: H:K.132, H:K.132, H:K.132, H:K.132, H:D.192, H:E.196, E:S.253, E:S.253 X9W.24: 14 residues within 4Å: Chain F: E.232, I.236, I.252, S.253, A.256 Chain K: A.133, P.134, D.192, E.196, L.200, C.201 Ligands: MG.42, MG.43, NDP.44 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain F Hydrogen bonds: K:A.133, K:D.192, K:E.196, F:S.253 Water bridges: K:K.132, K:K.132, K:D.192, K:E.196, K:E.196 X9W.27: 13 residues within 4Å: Chain D: E.232, I.236, I.252, S.253, A.256 Chain G: A.133, P.134, D.192, E.196, C.201 Ligands: MG.25, MG.26, NDP.28 9 PLIP interactions: 6 interactions with chain G, 3 interactions with chain D Hydrogen bonds: G:E.196, G:E.196, D:S.253 Water bridges: G:K.132, G:K.132, G:E.196, G:E.196, D:S.253, D:S.253 X9W.29: 13 residues within 4Å: Chain E: A.133, P.134, D.192, E.196, C.201 Chain H: E.232, I.236, I.252, S.253, A.256 Ligands: MG.17, MG.18, NDP.19 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:A.133, E:D.192, E:E.196, H:S.253 Water bridges: E:K.132, H:S.253 X9W.36: 14 residues within 4Å: Chain I: E.232, I.236, I.252, S.253, A.256 Chain J: A.133, P.134, D.192, E.196, L.200, C.201 Ligands: MG.38, MG.39, NDP.40 8 PLIP interactions: 3 interactions with chain I, 5 interactions with chain J Hydrogen bonds: I:S.253, I:A.256, J:A.133, J:D.192, J:E.196 Water bridges: I:S.253, J:K.132, J:D.192 X9W.37: 13 residues within 4Å: Chain I: A.133, P.134, D.192, E.196, C.201 Chain J: E.232, I.236, I.252, S.253, A.256 Ligands: MG.33, MG.34, NDP.35 7 PLIP interactions: 3 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:S.253, J:A.256, I:E.196, I:E.196 Water bridges: J:S.253, I:K.132, I:D.192 X9W.41: 13 residues within 4Å: Chain F: A.133, P.134, D.192, E.196, C.201 Chain K: E.232, I.236, I.252, S.253, A.256 Ligands: MG.21, MG.22, NDP.23 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain K Hydrogen bonds: F:A.133, F:D.192, F:E.196, K:S.253 Water bridges: F:H.109, F:K.132, F:D.192, F:E.196, F:E.196, K:S.253, K:S.253 X9W.45: 14 residues within 4Å: Chain A: A.133, P.134, D.192, E.196, L.200, C.201 Chain L: E.232, I.236, I.252, S.253, A.256 Ligands: MG.1, MG.2, NDP.3 9 PLIP interactions: 1 interactions with chain L, 8 interactions with chain A Hydrogen bonds: L:S.253, A:A.133, A:D.192, A:E.196 Water bridges: A:H.109, A:K.132, A:D.192, A:E.196, A:E.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, X. et al., Mapping of the Reaction Trajectory catalyzed by Class I Ketol-Acid Reductoisomerase. Acs Catalysis (2024)

Release Date

2024-04-24

Peptides

Ketol-acid reductoisomerase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
H

C
K

D
I

E
D

F
G

G
J

H
E

I
L

J
C

K
F

L
A

Ketol-acid reductoisomerase

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