SMTL ID : 6jqn.1

Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and OCoA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: R.27, I.161, N.162, A.163, F.164, N.165, K.188, P.189, A.190, T.191, F.237, T.238, G.239, S.240, T.243, L.247, E.263, A.264, D.265, C.302, E.402, F.404, H.479 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.238 Hydrogen bonds: A:N.162, A:F.164, A:K.188, A:T.191, A:S.240, A:T.243, A:E.263, A:E.402 Salt bridges: A:R.27, A:K.188 NAP.3: 24 residues within 4Å: Chain B: R.27, I.161, N.162, A.163, F.164, N.165, K.188, P.189, A.190, T.191, F.237, T.238, G.239, S.240, T.243, L.247, E.263, A.264, D.265, C.302, E.402, F.404, L.430, H.479 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.238 Hydrogen bonds: B:N.162, B:N.165, B:K.188, B:T.191, B:S.240, B:E.263, B:E.263 Salt bridges: B:R.27, B:K.188 NAP.5: 24 residues within 4Å: Chain C: R.27, I.161, N.162, A.163, F.164, N.165, K.188, P.189, A.190, T.191, F.237, T.238, G.239, S.240, T.243, L.247, E.263, A.264, D.265, C.302, E.402, F.404, L.430, H.479 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.238 Hydrogen bonds: C:N.162, C:N.165, C:K.188, C:T.191, C:S.240, C:E.263, C:E.263 Salt bridges: C:R.27, C:K.188 NAP.7: 24 residues within 4Å: Chain D: R.27, I.161, N.162, A.163, F.164, N.165, K.188, P.189, A.190, T.191, F.237, T.238, G.239, S.240, T.243, L.247, E.263, A.264, D.265, C.302, E.402, F.404, L.430, H.479 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:T.238 Hydrogen bonds: D:N.162, D:F.164, D:K.188, D:T.191, D:S.240, D:T.243, D:E.263 Salt bridges: D:R.27, D:K.188 NAP.9: 24 residues within 4Å: Chain E: R.27, I.161, N.162, A.163, F.164, N.165, K.188, P.189, A.190, T.191, F.237, T.238, G.239, S.240, T.243, L.247, E.263, A.264, D.265, C.302, E.402, F.404, L.430, H.479 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:T.238 Hydrogen bonds: E:N.162, E:N.165, E:K.188, E:T.191, E:S.240, E:E.263, E:E.263 Salt bridges: E:R.27, E:K.188 NAP.12: 24 residues within 4Å: Chain F: R.27, I.161, N.162, A.163, F.164, N.165, K.188, P.189, A.190, T.191, F.237, T.238, G.239, S.240, T.243, L.247, E.263, A.264, D.265, C.302, E.402, F.404, L.430, H.479 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:T.238 Hydrogen bonds: F:N.162, F:F.164, F:N.165, F:K.188, F:T.191, F:S.240, F:T.243, F:E.263, F:E.402 Salt bridges: F:R.27, F:K.188

6 x CO8: OCTANOYL-COENZYME A(Non-covalent)

CO8.2: 17 residues within 4Å: Chain A: F.570, H.573, F.584, V.588, V.589, G.591, R.620, F.621, I.622, P.624 Chain B: R.123, F.534, V.603, A.612, N.613, Y.614, K.643 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.570, A:F.570, A:F.621, B:F.534, B:V.603, B:N.613, B:Y.614 Hydrogen bonds: A:G.591, A:I.622, B:R.123, B:N.613, B:Y.614, B:Y.614 Salt bridges: A:R.620, B:K.643 CO8.4: 17 residues within 4Å: Chain A: R.123, A.599, V.603, V.610, A.612, N.613, Y.614, K.643 Chain B: F.570, H.573, F.584, V.588, G.591, R.620, F.621, I.622, P.624 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.599, A:V.610, A:A.612, A:N.613, A:Y.614, B:F.570, B:F.570, B:F.570, B:F.621 Hydrogen bonds: A:N.613, A:Y.614, B:F.621, B:I.622 Salt bridges: A:K.643, B:R.620 CO8.6: 21 residues within 4Å: Chain C: F.570, H.573, F.584, V.589, G.591, R.620, F.621, I.622, P.624, L.672 Chain D: R.123, A.599, F.602, V.603, V.610, A.612, N.613, Y.614, K.643, I.675, L.678 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:F.570, C:F.570, C:F.621, D:A.599, D:F.602, D:V.610, D:A.612, D:N.613, D:I.675, D:L.678 Hydrogen bonds: C:I.622, D:Y.614 Salt bridges: C:R.620, D:K.643 CO8.8: 19 residues within 4Å: Chain C: F.534, V.603, A.612, N.613, Y.614, K.643, L.678 Chain D: F.570, H.573, F.584, V.588, V.589, G.591, R.620, F.621, I.622, E.623, P.624, L.672 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:F.534, C:V.603, C:A.612, C:N.613, C:Y.614, D:F.570, D:F.570, D:F.584 Hydrogen bonds: C:N.613, C:Y.614, C:Y.614, D:G.591, D:F.621 Salt bridges: C:K.643, D:R.620 CO8.10: 20 residues within 4Å: Chain E: F.570, H.573, F.584, V.588, V.589, Y.592, R.620, F.621, I.622, L.672 Chain F: R.123, A.599, V.603, V.610, A.612, N.613, Y.614, K.643, I.675, L.678 16 PLIP interactions: 9 interactions with chain F, 7 interactions with chain E Hydrophobic interactions: F:A.599, F:V.610, F:A.612, F:N.613, F:I.675, F:L.678, E:F.570, E:F.570, E:Y.592, E:F.621 Hydrogen bonds: F:N.613, F:Y.614, E:I.622, E:I.622 Salt bridges: F:K.643, E:R.620 CO8.11: 20 residues within 4Å: Chain E: R.123, A.599, F.602, V.603, V.610, A.612, N.613, Y.614, K.643, I.675 Chain F: F.570, H.573, F.584, V.588, G.591, Y.592, R.620, F.621, I.622, P.624 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:A.599, E:F.602, E:V.603, E:V.610, E:N.613, E:Y.614, E:I.675, F:F.570, F:F.570, F:F.584, F:Y.592 Hydrogen bonds: E:R.123, E:Y.614, E:Y.614 Salt bridges: E:K.643, F:R.620

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sathyanarayanan, N. et al., Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun (2019)

Release Date

2019-09-11

Peptides

Bifunctional protein PaaZ: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Bifunctional protein PaaZ

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