SMTL ID : 2ihw.1

Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component in the branched-chain alpha-ketoacid dehydrogenase complex (BCKDC), apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-24-mer

Ligands

48 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 9 residues within 4Å: Chain A: M.47, L.134, P.191, V.192, L.194, I.200 Chain B: F.56, H.232 Ligands: ACT.2 Ligand excluded by PLIP ACT.2: 7 residues within 4Å: Chain A: D.129, L.134, S.179 Chain B: F.56, H.232, G.237 Ligands: ACT.1 Ligand excluded by PLIP ACT.5: 8 residues within 4Å: Chain B: M.47, L.134, P.191, V.192, L.194, I.200 Chain C: F.56 Ligands: ACT.6 Ligand excluded by PLIP ACT.6: 6 residues within 4Å: Chain B: D.129, L.134 Chain C: H.232, D.236, G.237 Ligands: ACT.5 Ligand excluded by PLIP ACT.8: 9 residues within 4Å: Chain A: F.56 Chain C: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.9 Ligand excluded by PLIP ACT.9: 7 residues within 4Å: Chain A: F.56, H.232, D.236, G.237 Chain C: D.129, L.134 Ligands: ACT.8 Ligand excluded by PLIP ACT.11: 8 residues within 4Å: Chain D: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.12 Ligand excluded by PLIP ACT.12: 7 residues within 4Å: Chain D: D.129, L.134 Chain E: F.56, H.232, D.236, G.237 Ligands: ACT.11 Ligand excluded by PLIP ACT.14: 8 residues within 4Å: Chain E: M.47, P.191, V.192, L.194, I.200 Chain F: F.56, H.232 Ligands: ACT.15 Ligand excluded by PLIP ACT.15: 7 residues within 4Å: Chain E: D.129, L.134, S.179 Chain F: H.232, D.236, G.237 Ligands: ACT.14 Ligand excluded by PLIP ACT.18: 7 residues within 4Å: Chain D: F.56 Chain F: M.47, P.191, V.192, L.194, I.200 Ligands: ACT.19 Ligand excluded by PLIP ACT.19: 6 residues within 4Å: Chain D: H.232, D.236, G.237 Chain F: D.129, L.134 Ligands: ACT.18 Ligand excluded by PLIP ACT.21: 9 residues within 4Å: Chain G: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Chain O: F.56 Ligands: ACT.22 Ligand excluded by PLIP ACT.22: 7 residues within 4Å: Chain G: D.129, L.134 Chain O: F.56, H.232, D.236, G.237 Ligands: ACT.21 Ligand excluded by PLIP ACT.25: 8 residues within 4Å: Chain H: M.47, L.134, P.191, V.192, L.194, I.200 Chain X: F.56 Ligands: ACT.26 Ligand excluded by PLIP ACT.26: 6 residues within 4Å: Chain H: D.129, L.134 Chain X: H.232, D.236, G.237 Ligands: ACT.25 Ligand excluded by PLIP ACT.29: 9 residues within 4Å: Chain I: M.47, L.134, P.191, V.192, L.194, I.200 Chain J: F.56, H.232 Ligands: ACT.30 Ligand excluded by PLIP ACT.30: 7 residues within 4Å: Chain I: D.129, L.134, S.179 Chain J: F.56, H.232, G.237 Ligands: ACT.29 Ligand excluded by PLIP ACT.33: 8 residues within 4Å: Chain J: M.47, L.134, P.191, V.192, L.194, I.200 Chain K: F.56 Ligands: ACT.34 Ligand excluded by PLIP ACT.34: 6 residues within 4Å: Chain J: D.129, L.134 Chain K: H.232, D.236, G.237 Ligands: ACT.33 Ligand excluded by PLIP ACT.36: 9 residues within 4Å: Chain I: F.56 Chain K: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.37 Ligand excluded by PLIP ACT.37: 7 residues within 4Å: Chain I: F.56, H.232, D.236, G.237 Chain K: D.129, L.134 Ligands: ACT.36 Ligand excluded by PLIP ACT.39: 8 residues within 4Å: Chain L: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.40 Ligand excluded by PLIP ACT.40: 7 residues within 4Å: Chain L: D.129, L.134 Chain M: F.56, H.232, D.236, G.237 Ligands: ACT.39 Ligand excluded by PLIP ACT.42: 8 residues within 4Å: Chain M: M.47, P.191, V.192, L.194, I.200 Chain N: F.56, H.232 Ligands: ACT.43 Ligand excluded by PLIP ACT.43: 7 residues within 4Å: Chain M: D.129, L.134, S.179 Chain N: H.232, D.236, G.237 Ligands: ACT.42 Ligand excluded by PLIP ACT.46: 7 residues within 4Å: Chain L: F.56 Chain N: M.47, P.191, V.192, L.194, I.200 Ligands: ACT.47 Ligand excluded by PLIP ACT.47: 6 residues within 4Å: Chain L: H.232, D.236, G.237 Chain N: D.129, L.134 Ligands: ACT.46 Ligand excluded by PLIP ACT.49: 9 residues within 4Å: Chain O: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Chain W: F.56 Ligands: ACT.50 Ligand excluded by PLIP ACT.50: 7 residues within 4Å: Chain O: D.129, L.134 Chain W: F.56, H.232, D.236, G.237 Ligands: ACT.49 Ligand excluded by PLIP ACT.53: 8 residues within 4Å: Chain H: F.56 Chain P: M.47, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.54 Ligand excluded by PLIP ACT.54: 6 residues within 4Å: Chain H: H.232, D.236, G.237 Chain P: D.129, L.134 Ligands: ACT.53 Ligand excluded by PLIP ACT.57: 9 residues within 4Å: Chain Q: M.47, L.134, P.191, V.192, L.194, I.200 Chain R: F.56, H.232 Ligands: ACT.58 Ligand excluded by PLIP ACT.58: 7 residues within 4Å: Chain Q: D.129, L.134, S.179 Chain R: F.56, H.232, G.237 Ligands: ACT.57 Ligand excluded by PLIP ACT.61: 8 residues within 4Å: Chain R: M.47, L.134, P.191, V.192, L.194, I.200 Chain S: F.56 Ligands: ACT.62 Ligand excluded by PLIP ACT.62: 6 residues within 4Å: Chain R: D.129, L.134 Chain S: H.232, D.236, G.237 Ligands: ACT.61 Ligand excluded by PLIP ACT.64: 9 residues within 4Å: Chain Q: F.56 Chain S: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.65 Ligand excluded by PLIP ACT.65: 7 residues within 4Å: Chain Q: F.56, H.232, D.236, G.237 Chain S: D.129, L.134 Ligands: ACT.64 Ligand excluded by PLIP ACT.67: 8 residues within 4Å: Chain T: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.68 Ligand excluded by PLIP ACT.68: 7 residues within 4Å: Chain T: D.129, L.134 Chain U: F.56, H.232, D.236, G.237 Ligands: ACT.67 Ligand excluded by PLIP ACT.70: 8 residues within 4Å: Chain U: M.47, P.191, V.192, L.194, I.200 Chain V: F.56, H.232 Ligands: ACT.71 Ligand excluded by PLIP ACT.71: 7 residues within 4Å: Chain U: D.129, L.134, S.179 Chain V: H.232, D.236, G.237 Ligands: ACT.70 Ligand excluded by PLIP ACT.74: 7 residues within 4Å: Chain T: F.56 Chain V: M.47, P.191, V.192, L.194, I.200 Ligands: ACT.75 Ligand excluded by PLIP ACT.75: 6 residues within 4Å: Chain T: H.232, D.236, G.237 Chain V: D.129, L.134 Ligands: ACT.74 Ligand excluded by PLIP ACT.77: 9 residues within 4Å: Chain G: F.56 Chain W: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.78 Ligand excluded by PLIP ACT.78: 7 residues within 4Å: Chain G: F.56, H.232, D.236, G.237 Chain W: D.129, L.134 Ligands: ACT.77 Ligand excluded by PLIP ACT.81: 8 residues within 4Å: Chain P: F.56 Chain X: M.47, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.82 Ligand excluded by PLIP ACT.82: 6 residues within 4Å: Chain P: H.232, D.236, G.237 Chain X: D.129, L.134 Ligands: ACT.81 Ligand excluded by PLIP

36 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: K.190 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.211 Chain C: R.211 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: H.55, K.190 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: H.55 Chain C: K.190 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain D: K.190 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain E: H.55, K.190 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain E: R.211 Chain F: R.211 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain F: K.190 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.51, CL.79 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain G: K.190 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain H: H.55 Chain P: K.190 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.56, CL.84 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain I: K.190 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain I: R.211 Chain K: R.211 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain J: H.55, K.190 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain I: H.55 Chain K: K.190 Ligand excluded by PLIP CL.41: 1 residues within 4Å: Chain L: K.190 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain M: H.55, K.190 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain M: R.211 Chain N: R.211 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain N: K.190 Ligand excluded by PLIP CL.51: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.23, CL.79 Ligand excluded by PLIP CL.52: 1 residues within 4Å: Chain O: K.190 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain P: H.55 Chain X: K.190 Ligand excluded by PLIP CL.56: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.28, CL.84 Ligand excluded by PLIP CL.59: 1 residues within 4Å: Chain Q: K.190 Ligand excluded by PLIP CL.60: 2 residues within 4Å: Chain Q: R.211 Chain S: R.211 Ligand excluded by PLIP CL.63: 2 residues within 4Å: Chain R: H.55, K.190 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain Q: H.55 Chain S: K.190 Ligand excluded by PLIP CL.69: 1 residues within 4Å: Chain T: K.190 Ligand excluded by PLIP CL.72: 2 residues within 4Å: Chain U: H.55, K.190 Ligand excluded by PLIP CL.73: 2 residues within 4Å: Chain U: R.211 Chain V: R.211 Ligand excluded by PLIP CL.76: 1 residues within 4Å: Chain V: K.190 Ligand excluded by PLIP CL.79: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.23, CL.51 Ligand excluded by PLIP CL.80: 1 residues within 4Å: Chain W: K.190 Ligand excluded by PLIP CL.83: 2 residues within 4Å: Chain H: K.190 Chain X: H.55 Ligand excluded by PLIP CL.84: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.28, CL.56 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, M. et al., A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex. Embo J. (2006)

Release Date

2006-12-26

Peptides

Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex: ABCDEFGHIJKLMNOPQRSTUVWX

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
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Q
A

R
B

S
C

T
D

U
E

V
F

W
G

X
H

Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex

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