SMTL ID : 1eab.1

ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-24-mer

Ligands

24 x COA: COENZYME A(Non-covalent)

COA.1: 17 residues within 4Å: Chain E: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:A.139, E:A.143 Hydrogen bonds: E:V.72, E:L.73, E:R.147, E:R.147, E:S.189, E:A.191 Water bridges: E:D.114, E:S.165, E:H.168 Salt bridges: E:K.69, E:K.69 COA.3: 17 residues within 4Å: Chain G: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:A.139, G:A.143 Hydrogen bonds: G:V.72, G:L.73, G:R.147, G:R.147, G:S.189, G:A.191 Water bridges: G:D.114, G:S.165, G:H.168 Salt bridges: G:K.69, G:K.69 COA.5: 17 residues within 4Å: Chain H: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:A.139, H:A.143 Hydrogen bonds: H:T.71, H:V.72, H:L.73, H:R.147, H:R.147, H:S.189, H:A.191 Water bridges: H:D.114, H:S.165, H:H.168 Salt bridges: H:K.69, H:K.69 COA.7: 17 residues within 4Å: Chain F: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:A.139, F:A.143 Hydrogen bonds: F:T.71, F:V.72, F:L.73, F:R.147, F:R.147, F:S.189, F:A.191 Water bridges: F:D.114, F:S.165, F:H.168 Salt bridges: F:K.69, F:K.69 COA.9: 17 residues within 4Å: Chain I: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:A.139, I:A.143 Hydrogen bonds: I:T.71, I:V.72, I:L.73, I:R.147, I:R.147, I:S.189, I:A.191 Water bridges: I:D.114, I:S.165, I:H.168 Salt bridges: I:K.69, I:K.69 COA.11: 17 residues within 4Å: Chain K: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:A.139, K:A.143 Hydrogen bonds: K:V.72, K:L.73, K:R.147, K:R.147, K:S.189, K:A.191 Water bridges: K:D.114, K:S.165, K:H.168 Salt bridges: K:K.69, K:K.69 COA.13: 17 residues within 4Å: Chain L: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:A.139, L:A.143 Hydrogen bonds: L:T.71, L:V.72, L:L.73, L:R.147, L:R.147, L:S.189, L:A.191 Water bridges: L:D.114, L:S.165, L:H.168 Salt bridges: L:K.69, L:K.69 COA.15: 17 residues within 4Å: Chain J: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:A.139, J:A.143 Hydrogen bonds: J:V.72, J:L.73, J:R.147, J:R.147, J:S.189, J:A.191 Water bridges: J:D.114, J:S.165, J:H.168 Salt bridges: J:K.69, J:K.69 COA.17: 17 residues within 4Å: Chain A: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.139, A:A.143 Hydrogen bonds: A:V.72, A:L.73, A:R.147, A:R.147, A:S.189, A:A.191 Water bridges: A:D.114, A:S.165, A:H.168 Salt bridges: A:K.69, A:K.69 COA.19: 17 residues within 4Å: Chain C: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.139, C:A.143 Hydrogen bonds: C:T.71, C:V.72, C:L.73, C:R.147, C:R.147, C:S.189, C:A.191 Water bridges: C:D.114, C:S.165, C:H.168 Salt bridges: C:K.69, C:K.69 COA.21: 17 residues within 4Å: Chain D: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:A.139, D:A.143 Hydrogen bonds: D:T.71, D:V.72, D:L.73, D:R.147, D:R.147, D:S.189, D:A.191 Water bridges: D:D.114, D:S.165, D:H.168 Salt bridges: D:K.69, D:K.69 COA.23: 17 residues within 4Å: Chain B: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.139, B:A.143 Hydrogen bonds: B:V.72, B:L.73, B:R.147, B:R.147, B:S.189, B:A.191 Water bridges: B:D.114, B:S.165, B:H.168 Salt bridges: B:K.69, B:K.69 COA.25: 17 residues within 4Å: Chain Q: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain Q Hydrophobic interactions: Q:A.139, Q:A.143 Hydrogen bonds: Q:T.71, Q:V.72, Q:L.73, Q:R.147, Q:R.147, Q:S.189, Q:A.191 Water bridges: Q:D.114, Q:S.165, Q:H.168 Salt bridges: Q:K.69, Q:K.69 COA.27: 17 residues within 4Å: Chain S: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain S Hydrophobic interactions: S:A.139, S:A.143 Hydrogen bonds: S:T.71, S:V.72, S:L.73, S:R.147, S:R.147, S:S.189, S:A.191 Water bridges: S:D.114, S:S.165, S:H.168 Salt bridges: S:K.69, S:K.69 COA.29: 17 residues within 4Å: Chain T: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain T Hydrophobic interactions: T:A.139, T:A.143 Hydrogen bonds: T:V.72, T:L.73, T:R.147, T:R.147, T:S.189, T:A.191 Water bridges: T:D.114, T:S.165, T:H.168 Salt bridges: T:K.69, T:K.69 COA.31: 17 residues within 4Å: Chain R: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain R Hydrophobic interactions: R:A.139, R:A.143 Hydrogen bonds: R:V.72, R:L.73, R:R.147, R:R.147, R:S.189, R:A.191 Water bridges: R:D.114, R:S.165, R:H.168 Salt bridges: R:K.69, R:K.69 COA.33: 17 residues within 4Å: Chain U: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain U Hydrophobic interactions: U:A.139, U:A.143 Hydrogen bonds: U:V.72, U:L.73, U:R.147, U:R.147, U:S.189, U:A.191 Water bridges: U:D.114, U:S.165, U:H.168 Salt bridges: U:K.69, U:K.69 COA.35: 17 residues within 4Å: Chain W: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain W Hydrophobic interactions: W:A.139, W:A.143 Hydrogen bonds: W:T.71, W:V.72, W:L.73, W:R.147, W:R.147, W:S.189, W:A.191 Water bridges: W:D.114, W:S.165, W:H.168 Salt bridges: W:K.69, W:K.69 COA.37: 17 residues within 4Å: Chain X: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain X Hydrophobic interactions: X:A.139, X:A.143 Hydrogen bonds: X:V.72, X:L.73, X:R.147, X:R.147, X:S.189, X:A.191 Water bridges: X:D.114, X:S.165, X:H.168 Salt bridges: X:K.69, X:K.69 COA.39: 17 residues within 4Å: Chain V: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain V Hydrophobic interactions: V:A.139, V:A.143 Hydrogen bonds: V:T.71, V:V.72, V:L.73, V:R.147, V:R.147, V:S.189, V:A.191 Water bridges: V:D.114, V:S.165, V:H.168 Salt bridges: V:K.69, V:K.69 COA.41: 17 residues within 4Å: Chain M: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain M Hydrophobic interactions: M:A.139, M:A.143 Hydrogen bonds: M:T.71, M:V.72, M:L.73, M:R.147, M:R.147, M:S.189, M:A.191 Water bridges: M:D.114, M:S.165, M:H.168 Salt bridges: M:K.69, M:K.69 COA.43: 17 residues within 4Å: Chain O: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain O Hydrophobic interactions: O:A.139, O:A.143 Hydrogen bonds: O:V.72, O:L.73, O:R.147, O:R.147, O:S.189, O:A.191 Water bridges: O:D.114, O:S.165, O:H.168 Salt bridges: O:K.69, O:K.69 COA.45: 17 residues within 4Å: Chain P: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 13 PLIP interactions: 13 interactions with chain P Hydrophobic interactions: P:A.139, P:A.143 Hydrogen bonds: P:V.72, P:L.73, P:R.147, P:R.147, P:S.189, P:A.191 Water bridges: P:D.114, P:S.165, P:H.168 Salt bridges: P:K.69, P:K.69 COA.47: 17 residues within 4Å: Chain N: K.69, T.71, V.72, L.73, A.112, A.139, A.140, A.143, R.147, S.165, G.167, H.168, V.188, S.189, K.190, A.191, L.208 14 PLIP interactions: 14 interactions with chain N Hydrophobic interactions: N:A.139, N:A.143 Hydrogen bonds: N:T.71, N:V.72, N:L.73, N:R.147, N:R.147, N:S.189, N:A.191 Water bridges: N:D.114, N:S.165, N:H.168 Salt bridges: N:K.69, N:K.69

24 x LPM: 6,8-DIMERCAPTO-OCTANOIC ACID AMIDE(Non-covalent)

LPM.2: 9 residues within 4Å: Chain A: H.216 Chain E: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:N.30, E:L.119, E:N.179 Hydrogen bonds: E:N.30, E:N.179 LPM.4: 9 residues within 4Å: Chain B: H.216 Chain G: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:N.30, G:L.119, G:N.179 Hydrogen bonds: G:N.30, G:N.179 LPM.6: 9 residues within 4Å: Chain C: H.216 Chain H: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:N.30, H:L.119, H:N.179 Hydrogen bonds: H:N.30, H:N.179 LPM.8: 9 residues within 4Å: Chain D: H.216 Chain F: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:N.30, F:L.119, F:N.179 Hydrogen bonds: F:N.30, F:N.179 LPM.10: 9 residues within 4Å: Chain E: H.216 Chain I: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:N.30, I:L.119, I:N.179 Hydrogen bonds: I:N.30, I:N.179 LPM.12: 9 residues within 4Å: Chain F: H.216 Chain K: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:N.30, K:L.119, K:N.179 Hydrogen bonds: K:N.30, K:N.179 LPM.14: 9 residues within 4Å: Chain G: H.216 Chain L: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:N.30, L:L.119, L:N.179 Hydrogen bonds: L:N.30, L:N.179 LPM.16: 9 residues within 4Å: Chain H: H.216 Chain J: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:N.30, J:L.119, J:N.179 Hydrogen bonds: J:N.30, J:N.179 LPM.18: 9 residues within 4Å: Chain A: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain I: H.216 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.30, A:L.119, A:N.179 Hydrogen bonds: A:N.30, A:N.179 LPM.20: 9 residues within 4Å: Chain C: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain J: H.216 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.30, C:L.119, C:N.179 Hydrogen bonds: C:N.30, C:N.179 LPM.22: 9 residues within 4Å: Chain D: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain K: H.216 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.30, D:L.119, D:N.179 Hydrogen bonds: D:N.30, D:N.179 LPM.24: 9 residues within 4Å: Chain B: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain L: H.216 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.30, B:L.119, B:N.179 Hydrogen bonds: B:N.30, B:N.179 LPM.26: 9 residues within 4Å: Chain M: H.216 Chain Q: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain Q Hydrophobic interactions: Q:N.30, Q:L.119, Q:N.179 Hydrogen bonds: Q:N.30, Q:N.179 LPM.28: 9 residues within 4Å: Chain N: H.216 Chain S: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain S Hydrophobic interactions: S:N.30, S:L.119, S:N.179 Hydrogen bonds: S:N.30, S:N.179 LPM.30: 9 residues within 4Å: Chain O: H.216 Chain T: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain T Hydrophobic interactions: T:N.30, T:L.119, T:N.179 Hydrogen bonds: T:N.30, T:N.179 LPM.32: 9 residues within 4Å: Chain P: H.216 Chain R: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain R Hydrophobic interactions: R:N.30, R:L.119, R:N.179 Hydrogen bonds: R:N.30, R:N.179 LPM.34: 9 residues within 4Å: Chain Q: H.216 Chain U: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain U Hydrophobic interactions: U:N.30, U:L.119, U:N.179 Hydrogen bonds: U:N.30, U:N.179 LPM.36: 9 residues within 4Å: Chain R: H.216 Chain W: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain W Hydrophobic interactions: W:N.30, W:L.119, W:N.179 Hydrogen bonds: W:N.30, W:N.179 LPM.38: 9 residues within 4Å: Chain S: H.216 Chain X: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain X Hydrophobic interactions: X:N.30, X:L.119, X:N.179 Hydrogen bonds: X:N.30, X:N.179 LPM.40: 9 residues within 4Å: Chain T: H.216 Chain V: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 5 PLIP interactions: 5 interactions with chain V Hydrophobic interactions: V:N.30, V:L.119, V:N.179 Hydrogen bonds: V:N.30, V:N.179 LPM.42: 9 residues within 4Å: Chain M: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain U: H.216 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:N.30, M:L.119, M:N.179 Hydrogen bonds: M:N.30, M:N.179 LPM.44: 9 residues within 4Å: Chain O: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain V: H.216 5 PLIP interactions: 5 interactions with chain O Hydrophobic interactions: O:N.30, O:L.119, O:N.179 Hydrogen bonds: O:N.30, O:N.179 LPM.46: 9 residues within 4Å: Chain P: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain W: H.216 5 PLIP interactions: 5 interactions with chain P Hydrophobic interactions: P:N.30, P:L.119, P:N.179 Hydrogen bonds: P:N.30, P:N.179 LPM.48: 9 residues within 4Å: Chain N: N.30, L.31, L.119, V.121, P.176, I.177, N.179, I.185 Chain X: H.216 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:N.30, N:L.119, N:N.179 Hydrogen bonds: N:N.30, N:N.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mattevi, A. et al., Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p). Biochemistry (1993)

Release Date

1993-10-31

Peptides

DIHYDROLIPOYL-TRANSACETYLASE: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

S
A

T
A

U
A

V
A

W
A

X
A

DIHYDROLIPOYL-TRANSACETYLASE

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