SMTL ID : 2ii5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-24-mer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: M.47, P.191, V.192, L.194, I.200 Chain B: F.56 Ligands: ACT.2 Ligand excluded by PLIP ACT.2: 7 residues within 4Å: Chain A: D.129, L.134, S.179 Chain B: H.232, D.236, G.237 Ligands: ACT.1 Ligand excluded by PLIP ACT.6: 7 residues within 4Å: Chain B: M.47, A.127, P.191, V.192, L.194, I.200 Ligands: ACT.7 Ligand excluded by PLIP ACT.7: 6 residues within 4Å: Chain B: D.129, L.134 Chain C: H.232, D.236, G.237 Ligands: ACT.6 Ligand excluded by PLIP ACT.10: 8 residues within 4Å: Chain C: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.11 Ligand excluded by PLIP ACT.11: 7 residues within 4Å: Chain A: F.56, H.232, D.236, G.237 Chain C: D.129, L.134 Ligands: ACT.10 Ligand excluded by PLIP ACT.14: 7 residues within 4Å: Chain D: M.47, A.127, P.191, V.192, L.194, I.200 Ligands: ACT.15 Ligand excluded by PLIP ACT.15: 6 residues within 4Å: Chain D: D.129, L.134 Chain E: H.232, D.236, G.237 Ligands: ACT.14 Ligand excluded by PLIP ACT.19: 8 residues within 4Å: Chain E: M.47, A.127, P.191, V.192, L.194, I.200 Chain F: F.56 Ligands: ACT.20 Ligand excluded by PLIP ACT.20: 7 residues within 4Å: Chain E: D.129, L.134, S.179 Chain F: H.232, D.236, G.237 Ligands: ACT.19 Ligand excluded by PLIP ACT.23: 7 residues within 4Å: Chain D: F.56 Chain F: M.47, P.191, V.192, L.194, I.200 Ligands: ACT.24 Ligand excluded by PLIP ACT.24: 6 residues within 4Å: Chain D: H.232, D.236, G.237 Chain F: D.129, L.134 Ligands: ACT.23 Ligand excluded by PLIP ACT.27: 8 residues within 4Å: Chain G: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.28 Ligand excluded by PLIP ACT.28: 7 residues within 4Å: Chain G: D.129, L.134 Chain O: F.56, H.232, D.236, G.237 Ligands: ACT.27 Ligand excluded by PLIP ACT.32: 9 residues within 4Å: Chain H: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Chain X: F.56 Ligands: ACT.33 Ligand excluded by PLIP ACT.33: 6 residues within 4Å: Chain H: D.129, L.134 Chain X: H.232, D.236, G.237 Ligands: ACT.32 Ligand excluded by PLIP ACT.37: 7 residues within 4Å: Chain I: M.47, P.191, V.192, L.194, I.200 Chain J: F.56 Ligands: ACT.38 Ligand excluded by PLIP ACT.38: 7 residues within 4Å: Chain I: D.129, L.134, S.179 Chain J: H.232, D.236, G.237 Ligands: ACT.37 Ligand excluded by PLIP ACT.42: 7 residues within 4Å: Chain J: M.47, A.127, P.191, V.192, L.194, I.200 Ligands: ACT.43 Ligand excluded by PLIP ACT.43: 6 residues within 4Å: Chain J: D.129, L.134 Chain K: H.232, D.236, G.237 Ligands: ACT.42 Ligand excluded by PLIP ACT.46: 8 residues within 4Å: Chain K: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.47 Ligand excluded by PLIP ACT.47: 7 residues within 4Å: Chain I: F.56, H.232, D.236, G.237 Chain K: D.129, L.134 Ligands: ACT.46 Ligand excluded by PLIP ACT.50: 7 residues within 4Å: Chain L: M.47, A.127, P.191, V.192, L.194, I.200 Ligands: ACT.51 Ligand excluded by PLIP ACT.51: 6 residues within 4Å: Chain L: D.129, L.134 Chain M: H.232, D.236, G.237 Ligands: ACT.50 Ligand excluded by PLIP ACT.55: 8 residues within 4Å: Chain M: M.47, A.127, P.191, V.192, L.194, I.200 Chain N: F.56 Ligands: ACT.56 Ligand excluded by PLIP ACT.56: 7 residues within 4Å: Chain M: D.129, L.134, S.179 Chain N: H.232, D.236, G.237 Ligands: ACT.55 Ligand excluded by PLIP ACT.59: 7 residues within 4Å: Chain L: F.56 Chain N: M.47, P.191, V.192, L.194, I.200 Ligands: ACT.60 Ligand excluded by PLIP ACT.60: 6 residues within 4Å: Chain L: H.232, D.236, G.237 Chain N: D.129, L.134 Ligands: ACT.59 Ligand excluded by PLIP ACT.63: 8 residues within 4Å: Chain O: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.64 Ligand excluded by PLIP ACT.64: 7 residues within 4Å: Chain O: D.129, L.134 Chain W: F.56, H.232, D.236, G.237 Ligands: ACT.63 Ligand excluded by PLIP ACT.68: 9 residues within 4Å: Chain H: F.56 Chain P: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.69 Ligand excluded by PLIP ACT.69: 6 residues within 4Å: Chain H: H.232, D.236, G.237 Chain P: D.129, L.134 Ligands: ACT.68 Ligand excluded by PLIP ACT.73: 7 residues within 4Å: Chain Q: M.47, P.191, V.192, L.194, I.200 Chain R: F.56 Ligands: ACT.74 Ligand excluded by PLIP ACT.74: 7 residues within 4Å: Chain Q: D.129, L.134, S.179 Chain R: H.232, D.236, G.237 Ligands: ACT.73 Ligand excluded by PLIP ACT.78: 7 residues within 4Å: Chain R: M.47, A.127, P.191, V.192, L.194, I.200 Ligands: ACT.79 Ligand excluded by PLIP ACT.79: 6 residues within 4Å: Chain R: D.129, L.134 Chain S: H.232, D.236, G.237 Ligands: ACT.78 Ligand excluded by PLIP ACT.82: 8 residues within 4Å: Chain S: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.83 Ligand excluded by PLIP ACT.83: 7 residues within 4Å: Chain Q: F.56, H.232, D.236, G.237 Chain S: D.129, L.134 Ligands: ACT.82 Ligand excluded by PLIP ACT.86: 7 residues within 4Å: Chain T: M.47, A.127, P.191, V.192, L.194, I.200 Ligands: ACT.87 Ligand excluded by PLIP ACT.87: 6 residues within 4Å: Chain T: D.129, L.134 Chain U: H.232, D.236, G.237 Ligands: ACT.86 Ligand excluded by PLIP ACT.91: 8 residues within 4Å: Chain U: M.47, A.127, P.191, V.192, L.194, I.200 Chain V: F.56 Ligands: ACT.92 Ligand excluded by PLIP ACT.92: 7 residues within 4Å: Chain U: D.129, L.134, S.179 Chain V: H.232, D.236, G.237 Ligands: ACT.91 Ligand excluded by PLIP ACT.95: 7 residues within 4Å: Chain T: F.56 Chain V: M.47, P.191, V.192, L.194, I.200 Ligands: ACT.96 Ligand excluded by PLIP ACT.96: 6 residues within 4Å: Chain T: H.232, D.236, G.237 Chain V: D.129, L.134 Ligands: ACT.95 Ligand excluded by PLIP ACT.99: 8 residues within 4Å: Chain W: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.100 Ligand excluded by PLIP ACT.100: 7 residues within 4Å: Chain G: F.56, H.232, D.236, G.237 Chain W: D.129, L.134 Ligands: ACT.99 Ligand excluded by PLIP ACT.104: 9 residues within 4Å: Chain P: F.56 Chain X: M.47, A.127, L.134, P.191, V.192, L.194, I.200 Ligands: ACT.105 Ligand excluded by PLIP ACT.105: 6 residues within 4Å: Chain P: H.232, D.236, G.237 Chain X: D.129, L.134 Ligands: ACT.104 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.8: 1 residues within 4Å: Chain B: K.190 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain C: K.190 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: R.211 Chain E: R.211 Chain F: R.211 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain D: K.190 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain E: K.190 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain F: H.55, K.190 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.65, CL.101 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain G: K.190 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain H: K.190 Chain X: H.55 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.71, CL.107 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Chain I: K.190 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain I: R.211 Chain K: R.211 Ligand excluded by PLIP CL.44: 1 residues within 4Å: Chain J: K.190 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain K: K.190 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain L: R.211 Chain M: R.211 Chain N: R.211 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Chain L: K.190 Ligand excluded by PLIP CL.57: 1 residues within 4Å: Chain M: K.190 Ligand excluded by PLIP CL.61: 2 residues within 4Å: Chain N: H.55, K.190 Ligand excluded by PLIP CL.65: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.29, CL.101 Ligand excluded by PLIP CL.66: 1 residues within 4Å: Chain O: K.190 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain H: H.55 Chain P: K.190 Ligand excluded by PLIP CL.71: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.35, CL.107 Ligand excluded by PLIP CL.75: 1 residues within 4Å: Chain Q: K.190 Ligand excluded by PLIP CL.76: 2 residues within 4Å: Chain Q: R.211 Chain S: R.211 Ligand excluded by PLIP CL.80: 1 residues within 4Å: Chain R: K.190 Ligand excluded by PLIP CL.84: 1 residues within 4Å: Chain S: K.190 Ligand excluded by PLIP CL.88: 3 residues within 4Å: Chain T: R.211 Chain U: R.211 Chain V: R.211 Ligand excluded by PLIP CL.89: 1 residues within 4Å: Chain T: K.190 Ligand excluded by PLIP CL.93: 1 residues within 4Å: Chain U: K.190 Ligand excluded by PLIP CL.97: 2 residues within 4Å: Chain V: H.55, K.190 Ligand excluded by PLIP CL.101: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.29, CL.65 Ligand excluded by PLIP CL.102: 1 residues within 4Å: Chain W: K.190 Ligand excluded by PLIP CL.106: 2 residues within 4Å: Chain P: H.55 Chain X: K.190 Ligand excluded by PLIP CL.107: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.35, CL.71 Ligand excluded by PLIP

24 x CO6: ISOBUTYRYL-COENZYME A(Non-covalent)

CO6.5: 11 residues within 4Å: Chain A: R.71, S.86, F.87, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.86, A:S.86, A:N.180, A:G.204, A:I.206 Salt bridges: A:R.71 CO6.9: 11 residues within 4Å: Chain B: R.71, S.86, F.87, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.86, B:N.180, B:G.204, B:I.206 Salt bridges: B:R.71 CO6.13: 10 residues within 4Å: Chain C: R.71, S.86, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.86, C:S.86, C:N.180, C:G.204, C:I.206 Water bridges: C:F.87 Salt bridges: C:R.71, C:K.75 CO6.18: 10 residues within 4Å: Chain D: R.71, K.75, S.86, F.87, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.86, D:N.180, D:G.204, D:I.206 Salt bridges: D:R.71, D:K.75, D:K.84 CO6.22: 15 residues within 4Å: Chain E: R.71, K.75, K.84, S.86, F.87, M.88, I.126, A.127, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:I.126, E:N.180 Hydrogen bonds: E:R.71, E:R.71, E:S.86, E:S.86, E:Q.158, E:N.180, E:N.180, E:S.183, E:I.206 Salt bridges: E:R.71, E:K.75, E:K.84, E:K.84 CO6.26: 9 residues within 4Å: Chain F: R.71, S.86, F.87, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.86, F:S.86, F:N.180, F:N.180, F:S.183, F:I.206 Salt bridges: F:R.71 CO6.31: 10 residues within 4Å: Chain G: R.71, S.86, F.87, M.88, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:R.71, G:S.86, G:S.86, G:N.180, G:G.204, G:I.206 Salt bridges: G:R.71 CO6.36: 10 residues within 4Å: Chain H: R.71, S.86, F.87, M.88, N.180, G.182, S.183, G.204, T.205, I.206 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.86, H:S.86, H:F.87, H:M.88, H:N.180, H:N.180, H:I.206 Salt bridges: H:R.71 CO6.41: 11 residues within 4Å: Chain I: R.71, S.86, F.87, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:S.86, I:S.86, I:N.180, I:G.204, I:I.206 Salt bridges: I:R.71 CO6.45: 11 residues within 4Å: Chain J: R.71, S.86, F.87, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:S.86, J:N.180, J:G.204, J:I.206 Salt bridges: J:R.71 CO6.49: 10 residues within 4Å: Chain K: R.71, S.86, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:S.86, K:S.86, K:N.180, K:G.204, K:I.206 Water bridges: K:F.87 Salt bridges: K:R.71, K:K.75 CO6.54: 10 residues within 4Å: Chain L: R.71, K.75, S.86, F.87, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:S.86, L:N.180, L:G.204, L:I.206 Salt bridges: L:R.71, L:K.75, L:K.84 CO6.58: 15 residues within 4Å: Chain M: R.71, K.75, K.84, S.86, F.87, M.88, I.126, A.127, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 15 PLIP interactions: 15 interactions with chain M Hydrophobic interactions: M:I.126, M:N.180 Hydrogen bonds: M:R.71, M:R.71, M:S.86, M:S.86, M:Q.158, M:N.180, M:N.180, M:S.183, M:I.206 Salt bridges: M:R.71, M:K.75, M:K.84, M:K.84 CO6.62: 9 residues within 4Å: Chain N: R.71, S.86, F.87, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain N Hydrogen bonds: N:S.86, N:S.86, N:N.180, N:N.180, N:S.183, N:I.206 Salt bridges: N:R.71 CO6.67: 10 residues within 4Å: Chain O: R.71, S.86, F.87, M.88, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain O Hydrogen bonds: O:R.71, O:S.86, O:S.86, O:N.180, O:G.204, O:I.206 Salt bridges: O:R.71 CO6.72: 10 residues within 4Å: Chain P: R.71, S.86, F.87, M.88, N.180, G.182, S.183, G.204, T.205, I.206 8 PLIP interactions: 8 interactions with chain P Hydrogen bonds: P:S.86, P:S.86, P:F.87, P:M.88, P:N.180, P:N.180, P:I.206 Salt bridges: P:R.71 CO6.77: 11 residues within 4Å: Chain Q: R.71, S.86, F.87, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 6 PLIP interactions: 6 interactions with chain Q Hydrogen bonds: Q:S.86, Q:S.86, Q:N.180, Q:G.204, Q:I.206 Salt bridges: Q:R.71 CO6.81: 11 residues within 4Å: Chain R: R.71, S.86, F.87, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 5 PLIP interactions: 5 interactions with chain R Hydrogen bonds: R:S.86, R:N.180, R:G.204, R:I.206 Salt bridges: R:R.71 CO6.85: 10 residues within 4Å: Chain S: R.71, S.86, M.88, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 8 PLIP interactions: 8 interactions with chain S Hydrogen bonds: S:S.86, S:S.86, S:N.180, S:G.204, S:I.206 Water bridges: S:F.87 Salt bridges: S:R.71, S:K.75 CO6.90: 10 residues within 4Å: Chain T: R.71, K.75, S.86, F.87, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain T Hydrogen bonds: T:S.86, T:N.180, T:G.204, T:I.206 Salt bridges: T:R.71, T:K.75, T:K.84 CO6.94: 15 residues within 4Å: Chain U: R.71, K.75, K.84, S.86, F.87, M.88, I.126, A.127, Q.158, N.180, G.182, S.183, G.204, T.205, I.206 15 PLIP interactions: 15 interactions with chain U Hydrophobic interactions: U:I.126, U:N.180 Hydrogen bonds: U:R.71, U:R.71, U:S.86, U:S.86, U:Q.158, U:N.180, U:N.180, U:S.183, U:I.206 Salt bridges: U:R.71, U:K.75, U:K.84, U:K.84 CO6.98: 9 residues within 4Å: Chain V: R.71, S.86, F.87, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain V Hydrogen bonds: V:S.86, V:S.86, V:N.180, V:N.180, V:S.183, V:I.206 Salt bridges: V:R.71 CO6.103: 10 residues within 4Å: Chain W: R.71, S.86, F.87, M.88, N.180, G.182, S.183, G.204, T.205, I.206 7 PLIP interactions: 7 interactions with chain W Hydrogen bonds: W:R.71, W:S.86, W:S.86, W:N.180, W:G.204, W:I.206 Salt bridges: W:R.71 CO6.108: 10 residues within 4Å: Chain X: R.71, S.86, F.87, M.88, N.180, G.182, S.183, G.204, T.205, I.206 8 PLIP interactions: 8 interactions with chain X Hydrogen bonds: X:S.86, X:S.86, X:F.87, X:M.88, X:N.180, X:N.180, X:I.206 Salt bridges: X:R.71

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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