SMTL ID : 2ii4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-24-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: H.55, K.190 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain B: H.55 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain C: H.55, K.190 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.211 Chain B: R.211 Chain C: R.211 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain D: K.190 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain D: R.211 Chain E: R.211 Chain F: R.211 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain E: K.190 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain F: H.55, K.190 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.35, CL.55 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain G: H.55, K.190 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain H: H.55, K.190 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.39, CL.59 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain I: H.55, K.190 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain J: H.55 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain K: H.55, K.190 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain I: R.211 Chain J: R.211 Chain K: R.211 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain L: K.190 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain L: R.211 Chain M: R.211 Chain N: R.211 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain M: K.190 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain N: H.55, K.190 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.15, CL.55 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain O: H.55, K.190 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain P: H.55, K.190 Ligand excluded by PLIP CL.39: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.19, CL.59 Ligand excluded by PLIP CL.41: 2 residues within 4Å: Chain Q: H.55, K.190 Ligand excluded by PLIP CL.43: 1 residues within 4Å: Chain R: H.55 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain S: H.55, K.190 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain Q: R.211 Chain R: R.211 Chain S: R.211 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Chain T: K.190 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain T: R.211 Chain U: R.211 Chain V: R.211 Ligand excluded by PLIP CL.51: 1 residues within 4Å: Chain U: K.190 Ligand excluded by PLIP CL.53: 2 residues within 4Å: Chain V: H.55, K.190 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain G: R.211 Chain O: R.211 Chain W: R.211 Ligands: CL.15, CL.35 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain W: H.55, K.190 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain X: H.55, K.190 Ligand excluded by PLIP CL.59: 5 residues within 4Å: Chain H: R.211 Chain P: R.211 Chain X: R.211 Ligands: CL.19, CL.39 Ligand excluded by PLIP

24 x COA: COENZYME A(Non-covalent)

COA.2: 22 residues within 4Å: Chain A: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain B: H.232, G.237 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.126, A:M.128, A:N.180 Hydrogen bonds: A:S.86, A:S.86, A:D.129, A:Q.158, A:S.179, A:N.180, A:N.180, A:N.180, A:S.183, A:I.206 Water bridges: A:M.88, A:S.183, B:G.237, B:A.238 Salt bridges: A:R.71, A:K.75 COA.4: 21 residues within 4Å: Chain B: R.71, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain C: H.232, G.237 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.126, B:M.128, B:N.180 Hydrogen bonds: B:S.86, B:S.86, B:D.129, B:Q.158, B:S.179, B:N.180, B:N.180, B:N.180, B:S.183, B:I.206, C:A.238 Water bridges: B:F.87, B:M.88 Salt bridges: B:R.71 COA.7: 21 residues within 4Å: Chain A: H.232, G.237 Chain C: R.71, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:N.180 Hydrogen bonds: C:R.71, C:R.71, C:S.86, C:S.86, C:D.129, C:Q.158, C:S.179, C:N.180, C:N.180, C:S.183, C:G.204, C:I.206, A:A.238 Water bridges: C:F.87, C:M.88, A:G.237 Salt bridges: C:R.71, C:K.75 COA.10: 24 residues within 4Å: Chain D: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, I.184, G.204, T.205, I.206, M.224 Chain E: H.232, G.237 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.126, D:N.180 Hydrogen bonds: D:S.86, D:S.86, D:D.129, D:Q.158, D:S.179, D:N.180, D:S.183, D:S.183, D:G.204, D:I.206 Water bridges: D:F.87, D:M.88, E:A.238 Salt bridges: D:R.71, D:K.75 COA.12: 21 residues within 4Å: Chain E: R.71, K.75, S.86, F.87, M.88, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain F: H.232, G.237 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:M.128, E:N.180 Hydrogen bonds: E:R.71, E:R.71, E:S.86, E:S.86, E:D.129, E:Q.158, E:S.179, E:N.180, E:S.183, E:S.183, E:G.204, E:I.206, F:A.238 Water bridges: E:M.88 Salt bridges: E:R.71, E:K.75 COA.14: 21 residues within 4Å: Chain D: H.232, G.237 Chain F: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 21 PLIP interactions: 19 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:I.126, F:M.128, F:N.180 Hydrogen bonds: F:R.71, F:R.71, F:S.86, F:S.86, F:D.129, F:Q.158, F:S.179, F:N.180, F:S.183, F:S.183, F:G.204, F:I.206 Water bridges: F:F.87, F:M.88, D:A.238, D:A.238 Salt bridges: F:R.71, F:K.75 COA.17: 22 residues within 4Å: Chain G: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain O: H.232, G.237 18 PLIP interactions: 16 interactions with chain G, 2 interactions with chain O Hydrophobic interactions: G:I.126, G:M.128 Hydrogen bonds: G:S.86, G:S.86, G:D.129, G:Q.158, G:S.179, G:N.180, G:N.180, G:S.183, G:G.204, G:I.206 Water bridges: G:F.87, G:M.88, O:A.238, O:A.238 Salt bridges: G:R.71, G:K.75 COA.20: 22 residues within 4Å: Chain H: R.71, K.84, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain X: H.232, G.237 19 PLIP interactions: 17 interactions with chain H, 2 interactions with chain X Hydrophobic interactions: H:I.126, H:M.128, H:Q.158 Hydrogen bonds: H:S.86, H:S.86, H:D.129, H:Q.158, H:S.179, H:N.180, H:S.183, H:S.183, H:G.204, H:I.206 Water bridges: H:F.87, H:M.88, X:A.238, X:A.238 Salt bridges: H:R.71, H:K.84 COA.22: 22 residues within 4Å: Chain I: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain J: H.232, G.237 19 PLIP interactions: 17 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:I.126, I:M.128, I:N.180 Hydrogen bonds: I:S.86, I:S.86, I:D.129, I:Q.158, I:S.179, I:N.180, I:N.180, I:N.180, I:S.183, I:I.206 Water bridges: I:M.88, I:S.183, J:G.237, J:A.238 Salt bridges: I:R.71, I:K.75 COA.24: 21 residues within 4Å: Chain J: R.71, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain K: H.232, G.237 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:I.126, J:M.128, J:N.180 Hydrogen bonds: J:S.86, J:S.86, J:D.129, J:Q.158, J:S.179, J:N.180, J:N.180, J:N.180, J:S.183, J:I.206, K:A.238 Water bridges: J:F.87, J:M.88 Salt bridges: J:R.71 COA.27: 21 residues within 4Å: Chain I: H.232, G.237 Chain K: R.71, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 19 PLIP interactions: 17 interactions with chain K, 2 interactions with chain I Hydrophobic interactions: K:N.180 Hydrogen bonds: K:R.71, K:R.71, K:S.86, K:S.86, K:D.129, K:Q.158, K:S.179, K:N.180, K:N.180, K:S.183, K:G.204, K:I.206, I:A.238 Water bridges: K:F.87, K:M.88, I:G.237 Salt bridges: K:R.71, K:K.75 COA.30: 24 residues within 4Å: Chain L: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, I.184, G.204, T.205, I.206, M.224 Chain M: H.232, G.237 17 PLIP interactions: 16 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:I.126, L:N.180 Hydrogen bonds: L:S.86, L:S.86, L:D.129, L:Q.158, L:S.179, L:N.180, L:S.183, L:S.183, L:G.204, L:I.206 Water bridges: L:F.87, L:M.88, M:A.238 Salt bridges: L:R.71, L:K.75 COA.32: 21 residues within 4Å: Chain M: R.71, K.75, S.86, F.87, M.88, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain N: H.232, G.237 18 PLIP interactions: 17 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:M.128, M:N.180 Hydrogen bonds: M:R.71, M:R.71, M:S.86, M:S.86, M:D.129, M:Q.158, M:S.179, M:N.180, M:S.183, M:S.183, M:G.204, M:I.206, N:A.238 Water bridges: M:M.88 Salt bridges: M:R.71, M:K.75 COA.34: 21 residues within 4Å: Chain L: H.232, G.237 Chain N: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 21 PLIP interactions: 19 interactions with chain N, 2 interactions with chain L Hydrophobic interactions: N:I.126, N:M.128, N:N.180 Hydrogen bonds: N:R.71, N:R.71, N:S.86, N:S.86, N:D.129, N:Q.158, N:S.179, N:N.180, N:S.183, N:S.183, N:G.204, N:I.206 Water bridges: N:F.87, N:M.88, L:A.238, L:A.238 Salt bridges: N:R.71, N:K.75 COA.37: 22 residues within 4Å: Chain O: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain W: H.232, G.237 18 PLIP interactions: 16 interactions with chain O, 2 interactions with chain W Hydrophobic interactions: O:I.126, O:M.128 Hydrogen bonds: O:S.86, O:S.86, O:D.129, O:Q.158, O:S.179, O:N.180, O:N.180, O:S.183, O:G.204, O:I.206 Water bridges: O:F.87, O:M.88, W:A.238, W:A.238 Salt bridges: O:R.71, O:K.75 COA.40: 22 residues within 4Å: Chain H: H.232, G.237 Chain P: R.71, K.84, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 19 PLIP interactions: 17 interactions with chain P, 2 interactions with chain H Hydrophobic interactions: P:I.126, P:M.128, P:Q.158 Hydrogen bonds: P:S.86, P:S.86, P:D.129, P:Q.158, P:S.179, P:N.180, P:S.183, P:S.183, P:G.204, P:I.206 Water bridges: P:F.87, P:M.88, H:A.238, H:A.238 Salt bridges: P:R.71, P:K.84 COA.42: 22 residues within 4Å: Chain Q: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain R: H.232, G.237 19 PLIP interactions: 17 interactions with chain Q, 2 interactions with chain R Hydrophobic interactions: Q:I.126, Q:M.128, Q:N.180 Hydrogen bonds: Q:S.86, Q:S.86, Q:D.129, Q:Q.158, Q:S.179, Q:N.180, Q:N.180, Q:N.180, Q:S.183, Q:I.206 Water bridges: Q:M.88, Q:S.183, R:G.237, R:A.238 Salt bridges: Q:R.71, Q:K.75 COA.44: 21 residues within 4Å: Chain R: R.71, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain S: H.232, G.237 17 PLIP interactions: 16 interactions with chain R, 1 interactions with chain S Hydrophobic interactions: R:I.126, R:M.128, R:N.180 Hydrogen bonds: R:S.86, R:S.86, R:D.129, R:Q.158, R:S.179, R:N.180, R:N.180, R:N.180, R:S.183, R:I.206, S:A.238 Water bridges: R:F.87, R:M.88 Salt bridges: R:R.71 COA.47: 21 residues within 4Å: Chain Q: H.232, G.237 Chain S: R.71, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 19 PLIP interactions: 2 interactions with chain Q, 17 interactions with chain S Hydrogen bonds: Q:A.238, S:R.71, S:R.71, S:S.86, S:S.86, S:D.129, S:Q.158, S:S.179, S:N.180, S:N.180, S:S.183, S:G.204, S:I.206 Water bridges: Q:G.237, S:F.87, S:M.88 Hydrophobic interactions: S:N.180 Salt bridges: S:R.71, S:K.75 COA.50: 24 residues within 4Å: Chain T: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, I.184, G.204, T.205, I.206, M.224 Chain U: H.232, G.237 17 PLIP interactions: 16 interactions with chain T, 1 interactions with chain U Hydrophobic interactions: T:I.126, T:N.180 Hydrogen bonds: T:S.86, T:S.86, T:D.129, T:Q.158, T:S.179, T:N.180, T:S.183, T:S.183, T:G.204, T:I.206 Water bridges: T:F.87, T:M.88, U:A.238 Salt bridges: T:R.71, T:K.75 COA.52: 21 residues within 4Å: Chain U: R.71, K.75, S.86, F.87, M.88, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 Chain V: H.232, G.237 18 PLIP interactions: 17 interactions with chain U, 1 interactions with chain V Hydrophobic interactions: U:M.128, U:N.180 Hydrogen bonds: U:R.71, U:R.71, U:S.86, U:S.86, U:D.129, U:Q.158, U:S.179, U:N.180, U:S.183, U:S.183, U:G.204, U:I.206, V:A.238 Water bridges: U:M.88 Salt bridges: U:R.71, U:K.75 COA.54: 21 residues within 4Å: Chain T: H.232, G.237 Chain V: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 21 PLIP interactions: 19 interactions with chain V, 2 interactions with chain T Hydrophobic interactions: V:I.126, V:M.128, V:N.180 Hydrogen bonds: V:R.71, V:R.71, V:S.86, V:S.86, V:D.129, V:Q.158, V:S.179, V:N.180, V:S.183, V:S.183, V:G.204, V:I.206 Water bridges: V:F.87, V:M.88, T:A.238, T:A.238 Salt bridges: V:R.71, V:K.75 COA.57: 22 residues within 4Å: Chain G: H.232, G.237 Chain W: R.71, K.75, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 18 PLIP interactions: 16 interactions with chain W, 2 interactions with chain G Hydrophobic interactions: W:I.126, W:M.128 Hydrogen bonds: W:S.86, W:S.86, W:D.129, W:Q.158, W:S.179, W:N.180, W:N.180, W:S.183, W:G.204, W:I.206 Water bridges: W:F.87, W:M.88, G:A.238, G:A.238 Salt bridges: W:R.71, W:K.75 COA.60: 22 residues within 4Å: Chain P: H.232, G.237 Chain X: R.71, K.84, S.86, F.87, M.88, I.126, A.127, M.128, D.129, L.134, L.154, Q.158, S.179, N.180, I.181, G.182, S.183, G.204, T.205, I.206 19 PLIP interactions: 17 interactions with chain X, 2 interactions with chain P Hydrophobic interactions: X:I.126, X:M.128, X:Q.158 Hydrogen bonds: X:S.86, X:S.86, X:D.129, X:Q.158, X:S.179, X:N.180, X:S.183, X:S.183, X:G.204, X:I.206 Water bridges: X:F.87, X:M.88, P:A.238, P:A.238 Salt bridges: X:R.71, X:K.84

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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