SMTL ID : 6jd1.1

Cryo-EM Structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) in complex with Mg2+, NADH, and CPD at pH7.5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

MG.1: 5 residues within 4Å: Chain A: D.191, L.192, E.195 Chain B: S.257 Ligands: 9TY.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.191, A:D.191, A:E.195, A:E.195 MG.2: 5 residues within 4Å: Chain A: R.130, D.191 Chain B: E.227, E.233 Ligands: 9TY.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.191 MG.3: 1 residues within 4Å: Ligands: NAI.4 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: D.191, L.192, E.195 Ligands: 9TY.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.191, B:D.191, B:D.191, B:E.195, B:E.195 MG.7: 4 residues within 4Å: Chain A: E.227 Chain B: R.130, D.191 Ligands: 9TY.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.191 MG.8: 1 residues within 4Å: Ligands: NAI.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.191, L.192, E.195 Ligands: 9TY.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.191, C:D.191, C:D.191, C:E.195 MG.12: 4 residues within 4Å: Chain C: R.130, D.191 Chain D: E.227 Ligands: 9TY.15 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.191 MG.13: 2 residues within 4Å: Chain C: V.46 Ligands: NAI.14 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain C: S.257 Chain D: D.191, L.192, E.195 Ligands: 9TY.20 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.191, D:D.191, D:D.191, D:E.195, D:E.195 MG.17: 4 residues within 4Å: Chain C: E.227 Chain D: R.130, D.191 Ligands: 9TY.20 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.191 MG.18: 1 residues within 4Å: Ligands: NAI.19 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain E: D.191, L.192, E.195 Ligands: 9TY.24 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.191, E:E.195 MG.22: 2 residues within 4Å: Chain E: V.46 Ligands: NAI.23 No protein-ligand interaction detected (PLIP) MG.25: 6 residues within 4Å: Chain E: R.130, D.191, S.194 Chain F: E.227, E.233 Ligands: 9TY.24 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.227, F:E.233, F:E.233 MG.26: 4 residues within 4Å: Chain F: D.191, L.192, E.195 Ligands: 9TY.30 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.191, F:D.191, F:D.191, F:E.195, F:E.195 MG.27: 5 residues within 4Å: Chain E: E.227, E.233 Chain F: R.130, D.191 Ligands: 9TY.30 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.191 MG.28: 1 residues within 4Å: Ligands: NAI.29 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain G: D.191, L.192, E.195 Ligands: 9TY.35 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.191, G:D.191, G:E.195, G:E.195 MG.32: 4 residues within 4Å: Chain G: R.130, D.191 Chain H: E.227 Ligands: 9TY.35 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.191 MG.33: 2 residues within 4Å: Chain G: V.46 Ligands: NAI.34 No protein-ligand interaction detected (PLIP) MG.36: 4 residues within 4Å: Chain H: D.191, L.192, E.195 Ligands: 9TY.40 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.191, H:D.191, H:E.195, H:E.195 MG.37: 4 residues within 4Å: Chain G: E.227 Chain H: R.130, D.191 Ligands: 9TY.40 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.191 MG.38: 1 residues within 4Å: Ligands: NAI.39 No protein-ligand interaction detected (PLIP) MG.41: 4 residues within 4Å: Chain I: D.191, L.192, E.195 Ligands: 9TY.45 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.191, I:D.191, I:D.191, I:E.195, I:E.195 MG.42: 4 residues within 4Å: Chain I: R.130, D.191 Chain J: E.227 Ligands: 9TY.45 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.191 MG.43: 1 residues within 4Å: Ligands: NAI.44 No protein-ligand interaction detected (PLIP) MG.46: 4 residues within 4Å: Chain J: D.191, L.192, E.195 Ligands: 9TY.50 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.191, J:D.191, J:D.191, J:E.195, J:E.195 MG.47: 4 residues within 4Å: Chain I: E.227 Chain J: R.130, D.191 Ligands: 9TY.50 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.191 MG.48: 1 residues within 4Å: Ligands: NAI.49 No protein-ligand interaction detected (PLIP) MG.51: 5 residues within 4Å: Chain K: D.191, L.192, E.195 Chain L: S.257 Ligands: 9TY.55 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.191, K:D.191, K:D.191, K:E.195, K:E.195 MG.52: 4 residues within 4Å: Chain K: R.130, D.191 Chain L: E.227 Ligands: 9TY.55 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.191 MG.53: 1 residues within 4Å: Ligands: NAI.54 No protein-ligand interaction detected (PLIP) MG.56: 5 residues within 4Å: Chain K: S.257 Chain L: D.191, L.192, E.195 Ligands: 9TY.60 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.191, L:D.191, L:E.195 MG.57: 5 residues within 4Å: Chain K: E.227, E.233 Chain L: R.130, D.191 Ligands: 9TY.60 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.191 MG.58: 1 residues within 4Å: Ligands: NAI.59 No protein-ligand interaction detected (PLIP)

12 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.4: 26 residues within 4Å: Chain A: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, I.64, L.77, I.78, P.79, D.80, V.82, V.86, K.90, A.106, S.107, P.129, M.131, V.132, G.133 Chain B: S.254 Ligands: MG.3, 9TY.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.26 Hydrogen bonds: A:Y.23, A:N.25, A:N.25, A:Q.26, A:Q.26, A:N.45, A:N.45, A:D.80, A:S.107 NAI.9: 25 residues within 4Å: Chain A: S.254 Chain B: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, I.64, L.77, I.78, P.79, D.80, V.82, V.86, A.106, S.107, P.129, M.131, V.132, G.133 Ligands: MG.8, 9TY.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.23, B:N.25, B:N.25, B:Q.26, B:Q.26, B:N.45, B:N.45, B:D.80, B:D.80 NAI.14: 24 residues within 4Å: Chain C: G.22, Y.23, G.24, N.25, Q.26, N.45, V.46, Y.50, I.64, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, M.131, V.132, G.133 Chain D: H.252, S.254 Ligands: MG.13, 9TY.15 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.23, C:N.25, C:N.25, C:Q.26, C:N.45, C:N.45, C:Y.50, C:D.80, C:D.80, C:S.107, C:V.132 NAI.19: 23 residues within 4Å: Chain C: H.252, S.254 Chain D: G.22, Y.23, G.24, N.25, Q.26, N.45, V.46, Y.50, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, M.131, V.132, G.133 Ligands: MG.18, 9TY.20 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.26 Hydrogen bonds: D:Y.23, D:N.25, D:N.25, D:Q.26, D:N.45, D:N.45, D:D.80, D:D.80, D:S.107, D:V.132, C:S.254 NAI.23: 23 residues within 4Å: Chain E: G.22, Y.23, G.24, N.25, Q.26, N.45, V.46, Y.50, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, M.131, V.132, G.133 Chain F: H.252, S.254 Ligands: MG.22, 9TY.24 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Y.23, E:N.25, E:N.25, E:Q.26, E:N.45, E:N.45, E:D.80, E:D.80, E:V.132 NAI.29: 23 residues within 4Å: Chain E: H.252, S.254 Chain F: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, M.131, V.132 Ligands: MG.28, 9TY.30 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:Q.26 Hydrogen bonds: F:N.25, F:N.25, F:Q.26, F:N.45, F:N.45, F:D.80, F:D.80, F:V.132 NAI.34: 24 residues within 4Å: Chain G: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, M.131, V.132, G.133 Chain H: H.252, S.254 Ligands: MG.33, 9TY.35 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:Y.23, G:G.24, G:N.25, G:N.25, G:Q.26, G:N.45, G:N.45, G:D.80, G:D.80, G:S.107 NAI.39: 25 residues within 4Å: Chain G: H.252, S.254 Chain H: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, I.64, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, M.131, V.132, G.133 Ligands: MG.38, 9TY.40 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:Y.23, H:G.24, H:N.25, H:N.25, H:Q.26, H:N.45, H:N.45, H:D.80, H:D.80, H:V.132 NAI.44: 27 residues within 4Å: Chain I: G.22, Y.23, G.24, N.25, Q.26, N.45, V.46, D.48, Y.50, L.77, I.78, P.79, D.80, V.82, V.86, K.90, A.106, S.107, P.129, R.130, M.131, V.132, G.133 Chain J: H.252, S.254 Ligands: MG.43, 9TY.45 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:Y.23, I:G.24, I:N.25, I:N.25, I:Q.26, I:N.45, I:D.48, I:D.80, I:D.80, I:S.107, I:V.132 NAI.49: 24 residues within 4Å: Chain I: S.254 Chain J: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, L.77, I.78, P.79, D.80, V.82, A.106, S.107, P.129, R.130, M.131, V.132, G.133 Ligands: MG.48, 9TY.50 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:N.25, J:N.25, J:N.25, J:Q.26, J:Q.26, J:N.45, J:N.45, J:D.80, J:D.80, J:V.132 NAI.54: 25 residues within 4Å: Chain K: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, I.64, L.77, I.78, P.79, D.80, V.82, V.86, A.106, S.107, P.129, M.131, V.132, G.133 Chain L: S.254 Ligands: MG.53, 9TY.55 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:Y.23, K:N.25, K:N.25, K:Q.26, K:N.45, K:D.80, K:D.80, K:V.132 NAI.59: 26 residues within 4Å: Chain K: S.254 Chain L: G.22, Y.23, G.24, N.25, Q.26, G.27, N.45, V.46, Y.50, I.64, L.77, I.78, P.79, D.80, V.82, V.86, A.106, S.107, P.129, R.130, M.131, V.132, G.133 Ligands: MG.58, 9TY.60 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:Q.26 Hydrogen bonds: L:Y.23, L:N.25, L:N.25, L:Q.26, L:Q.26, L:N.45, L:N.45, L:D.80

12 x 9TY: cyclopropane-1,1-dicarboxylic acid(Non-covalent)

9TY.5: 10 residues within 4Å: Chain A: S.107, R.130, D.191, E.195 Chain B: E.233, S.254, S.257 Ligands: MG.1, MG.2, NAI.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.257 Water bridges: B:S.254 Salt bridges: B:H.253 9TY.10: 11 residues within 4Å: Chain A: E.233, H.253, S.254, S.257 Chain B: S.107, R.130, D.191, E.195 Ligands: MG.6, MG.7, NAI.9 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.257, B:E.195, B:E.195 Water bridges: A:S.254 Salt bridges: A:H.253 9TY.15: 10 residues within 4Å: Chain C: S.107, R.130, D.191, L.192, E.195 Chain D: E.233, S.257 Ligands: MG.11, MG.12, NAI.14 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.257, C:E.195 Water bridges: D:S.254 Salt bridges: D:H.253 9TY.20: 10 residues within 4Å: Chain C: E.233, H.253, S.257 Chain D: S.107, R.130, D.191, E.195 Ligands: MG.16, MG.17, NAI.19 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:S.254 Salt bridges: C:H.253 Hydrogen bonds: D:E.195 9TY.24: 10 residues within 4Å: Chain E: S.107, R.130, D.191, E.195 Chain F: E.227, E.233, S.257 Ligands: MG.21, NAI.23, MG.25 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.130 9TY.30: 9 residues within 4Å: Chain E: E.233, S.254, S.257 Chain F: R.130, D.191, E.195 Ligands: MG.26, MG.27, NAI.29 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:E.195 Water bridges: E:S.254 Salt bridges: E:H.253 9TY.35: 9 residues within 4Å: Chain G: S.107, R.130, D.191, E.195 Chain H: S.254, S.257 Ligands: MG.31, MG.32, NAI.34 2 PLIP interactions: 2 interactions with chain H Water bridges: H:S.254 Salt bridges: H:H.253 9TY.40: 9 residues within 4Å: Chain G: S.254, S.257 Chain H: S.107, R.130, D.191, E.195 Ligands: MG.36, MG.37, NAI.39 2 PLIP interactions: 2 interactions with chain G Water bridges: G:S.254 Salt bridges: G:H.253 9TY.45: 9 residues within 4Å: Chain I: S.107, R.130, D.191, E.195 Chain J: E.233, S.257 Ligands: MG.41, MG.42, NAI.44 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Water bridges: J:S.254 Salt bridges: J:H.253 Hydrogen bonds: I:E.195 9TY.50: 10 residues within 4Å: Chain I: E.233, S.254, S.257 Chain J: S.107, R.130, D.191, E.195 Ligands: MG.46, MG.47, NAI.49 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:E.195 Water bridges: I:S.254 Salt bridges: I:H.253 9TY.55: 11 residues within 4Å: Chain K: S.107, R.130, D.191, L.192, E.195 Chain L: E.233, H.253, S.257 Ligands: MG.51, MG.52, NAI.54 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:S.257, K:R.130, K:E.195 Salt bridges: L:H.253 9TY.60: 10 residues within 4Å: Chain K: E.233, S.257 Chain L: S.107, R.130, D.191, L.192, E.195 Ligands: MG.56, MG.57, NAI.59 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:E.233, K:S.257, L:E.195 Water bridges: K:S.254 Salt bridges: K:H.253

Links

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Citation

Chen, C.Y. et al., Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase. J. Am. Chem. Soc. (2019)

Release Date

2019-04-17

Peptides

Putative ketol-acid reductoisomerase 2: ABCDEFGHIJKL

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

K
K

L
L

Putative ketol-acid reductoisomerase 2

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