SMTL ID : 7bvp.1

AdhE spirosome in extended conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 24 residues within 4Å: Chain A: I.112, V.113, P.114, T.115, T.116, N.117, H.141, T.195, G.196, G.197, G.199, M.200, A.203, V.214, G.215, A.216, G.217, C.248, E.337, L.339, H.369, L.419, T.420, L.421 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.113, A:T.115, A:G.197, A:E.337, A:L.421, A:L.421 NAD.2: 18 residues within 4Å: Chain A: D.489, F.491, A.520, D.521, G.548, S.549, D.552, T.599, T.600, T.603, S.605, F.610, V.612, K.621, L.640, L.648, F.716, H.739 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.603 Hydrogen bonds: A:D.489, A:A.520, A:D.521, A:D.521, A:G.548, A:S.549, A:S.549, A:D.552, A:T.599, A:T.603, A:K.621, A:K.621, A:L.640 NAD.4: 23 residues within 4Å: Chain B: I.112, V.113, P.114, T.115, T.116, N.117, P.140, H.141, P.142, S.180, G.196, G.197, M.200, A.203, V.214, G.215, A.216, C.248, E.337, L.339, H.369, L.419, L.421 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.115, B:P.140, B:S.180, B:G.197, B:G.199, B:E.337, B:L.421, B:L.421 NAD.5: 23 residues within 4Å: Chain B: D.489, F.491, L.492, A.520, D.521, G.548, S.549, P.550, D.552, T.599, T.600, T.603, S.605, T.608, F.610, V.612, K.621, L.640, L.648, H.659, F.716, H.739 Ligands: ZN.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.603 Hydrogen bonds: B:D.489, B:A.520, B:A.520, B:D.521, B:G.548, B:S.549, B:D.552, B:T.599, B:T.600, B:T.603, B:T.608, B:K.621, B:K.621, B:L.640 NAD.7: 23 residues within 4Å: Chain C: I.112, V.113, P.114, T.115, T.116, N.117, P.140, H.141, G.196, G.197, M.200, A.203, V.214, G.215, A.216, G.217, C.248, E.337, L.339, H.369, L.419, T.420, L.421 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.113, C:T.115, C:G.197, C:E.337, C:L.421, C:L.421 NAD.8: 22 residues within 4Å: Chain C: D.489, F.491, D.521, G.548, S.549, P.550, D.552, T.599, T.600, T.603, S.605, T.608, F.610, A.611, V.612, K.621, L.640, M.644, P.645, L.648, H.739 Ligands: ZN.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.603 Hydrogen bonds: C:D.489, C:A.520, C:G.548, C:S.549, C:D.552, C:T.599, C:T.599, C:T.603, C:K.621, C:K.621 NAD.10: 25 residues within 4Å: Chain D: I.112, V.113, P.114, T.115, T.116, N.117, S.139, P.140, H.141, G.196, G.197, G.199, M.200, A.203, V.214, G.215, A.216, G.217, C.248, E.337, L.339, H.369, L.419, T.420, L.421 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.115, D:P.140, D:G.197, D:E.337, D:L.421, D:L.421 NAD.11: 21 residues within 4Å: Chain D: D.489, F.491, L.492, D.521, G.547, G.548, S.549, P.550, D.552, T.599, T.600, T.603, S.605, T.608, F.610, V.612, K.621, L.640, L.648, H.739 Ligands: ZN.12 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:T.603 Hydrogen bonds: D:D.489, D:A.520, D:G.548, D:S.549, D:D.552, D:T.599, D:T.599, D:T.600, D:T.603, D:T.608, D:K.621, D:K.621 NAD.13: 26 residues within 4Å: Chain E: I.112, V.113, P.114, T.115, T.116, N.117, S.139, P.140, H.141, P.142, S.180, M.184, G.196, G.197, M.200, A.203, V.214, G.215, A.216, C.248, E.337, L.339, H.369, L.419, T.420, L.421 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:P.140, E:S.180, E:G.197, E:L.421, E:L.421 NAD.14: 20 residues within 4Å: Chain E: D.489, F.491, D.521, G.547, G.548, S.549, P.550, D.552, T.599, T.600, T.603, S.605, T.608, F.610, A.611, K.621, L.640, L.648, H.739 Ligands: ZN.15 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:T.603 Hydrogen bonds: E:D.489, E:A.520, E:D.521, E:G.548, E:S.549, E:D.552, E:T.599, E:T.599, E:T.600, E:T.600, E:T.603, E:T.608, E:K.621, E:H.739 NAD.16: 22 residues within 4Å: Chain F: I.112, V.113, P.114, T.115, N.117, S.139, P.140, H.141, G.196, G.197, G.199, M.200, V.214, G.215, A.216, C.248, E.337, L.339, H.369, L.419, T.420, L.421 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.214 Hydrogen bonds: F:V.113, F:T.115, F:P.140, F:G.197, F:E.337, F:L.421, F:L.421 NAD.17: 26 residues within 4Å: Chain F: D.489, F.491, A.520, D.521, G.547, G.548, S.549, P.550, D.552, T.599, T.600, T.603, S.605, T.608, F.610, V.612, K.621, L.640, V.641, D.643, M.644, P.645, L.648, F.716, H.739 Ligands: ZN.18 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:T.603 Hydrogen bonds: F:D.489, F:D.489, F:D.489, F:A.520, F:A.520, F:D.521, F:G.548, F:S.549, F:T.599, F:T.600, F:T.600, F:T.603, F:T.608, F:K.621, F:K.621 pi-Stacking: F:H.739

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.655, H.659, H.725, H.739, N.743 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.655, A:H.659, A:H.725, A:H.739 ZN.6: 6 residues within 4Å: Chain B: D.655, H.659, H.725, H.739, N.743 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.655, B:H.659, B:H.725, B:H.739 ZN.9: 6 residues within 4Å: Chain C: D.655, H.659, H.725, H.739, N.743 Ligands: NAD.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.655, C:H.659, C:H.725, C:H.739 ZN.12: 6 residues within 4Å: Chain D: D.655, H.659, H.725, H.739, N.743 Ligands: NAD.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.655, D:H.659, D:H.725, D:H.739 ZN.15: 6 residues within 4Å: Chain E: D.655, H.659, H.725, H.739, N.743 Ligands: NAD.14 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.655, E:H.659, E:H.725, E:H.739 ZN.18: 6 residues within 4Å: Chain F: D.655, H.659, H.725, H.739, N.743 Ligands: NAD.17 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.655, F:H.659, F:H.725, F:H.739

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, G. et al., Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling. Commun Biol (2020)

Release Date

2020-06-24

Peptides

Aldehyde-alcohol dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Aldehyde-alcohol dehydrogenase

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