SMTL ID : 3l8k.1

Crystal structure of a dihydrolipoyl dehydrogenase from Sulfolobus solfataricus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 24 residues within 4Å: Chain A: I.10, G.11, G.13, G.14, A.15, A.33, D.34, P.35, K.36, G.41, N.42, C.43, G.109, Y.110, V.111, A.139, S.140, G.141, A.142, V.273, P.275, G.307, D.308, A.319 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.15, A:N.42, A:N.42, A:C.43, A:V.111, A:V.111, A:A.142, A:D.308 Water bridges: A:G.13, A:G.14, A:G.14, A:G.16 ADP.3: 23 residues within 4Å: Chain B: I.10, G.11, G.13, G.14, A.15, A.33, D.34, P.35, K.36, G.41, N.42, C.43, G.109, Y.110, V.111, A.139, S.140, G.141, A.142, V.273, G.307, D.308, A.319 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.13, B:A.15, B:K.36, B:K.36, B:N.42, B:N.42, B:C.43, B:V.111, B:V.111, B:A.142, B:D.308 Water bridges: B:G.14, B:G.14, B:G.16, B:D.34, B:G.41, B:A.309 ADP.5: 24 residues within 4Å: Chain C: I.10, G.11, G.13, G.14, A.15, A.33, D.34, P.35, K.36, G.41, N.42, C.43, G.109, Y.110, V.111, A.139, S.140, G.141, A.142, V.273, P.275, G.307, D.308, A.319 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.15, C:N.42, C:N.42, C:C.43, C:V.111, C:V.111, C:A.142, C:D.308 Water bridges: C:G.13, C:G.14, C:G.14, C:G.16 ADP.7: 23 residues within 4Å: Chain D: I.10, G.11, G.13, G.14, A.15, A.33, D.34, P.35, K.36, G.41, N.42, C.43, G.109, Y.110, V.111, A.139, S.140, G.141, A.142, V.273, G.307, D.308, A.319 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:G.13, D:A.15, D:K.36, D:K.36, D:N.42, D:N.42, D:C.43, D:V.111, D:V.111, D:A.142, D:D.308 Water bridges: D:G.14, D:G.14, D:G.16, D:D.34, D:G.41, D:A.309

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: R.55, Q.59, R.63, V.414, H.415, Q.417, Y.418 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.59, A:Q.59, A:H.415, A:Q.417 Salt bridges: A:R.55, A:R.63, A:H.415 Water bridges: A:S.354, A:S.354 PO4.4: 7 residues within 4Å: Chain B: R.55, Q.59, R.63, V.414, H.415, Q.417, Y.418 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.59, B:H.415, B:Q.417 Salt bridges: B:R.55, B:R.63, B:H.415 Water bridges: B:R.55, B:S.354 PO4.6: 7 residues within 4Å: Chain C: R.55, Q.59, R.63, V.414, H.415, Q.417, Y.418 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.59, C:Q.59, C:H.415, C:Q.417 Salt bridges: C:R.55, C:R.63, C:H.415 Water bridges: C:S.354, C:S.354 PO4.8: 7 residues within 4Å: Chain D: R.55, Q.59, R.63, V.414, H.415, Q.417, Y.418 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.59, D:H.415, D:Q.417 Salt bridges: D:R.55, D:R.63, D:H.415 Water bridges: D:R.55, D:S.354

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Bonanno, J.B. et al., Crystal structure of a dihydrolipoyl dehydrogenase from Sulfolobus solfataricus. To be Published

Release Date

2010-02-09

Peptides

Dihydrolipoyl dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydrolipoyl dehydrogenase