SMTL ID : 6jqo.1

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

Coordinates

PDB Format Compare

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, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.238 Hydrogen bonds: A:N.162, A:T.191, A:S.240, A:T.243, A:E.263 Salt bridges: A:R.27, A:K.188 NAP.3: 22 residues within 4Å: Chain B: R.27, I.161, N.162, A.163, F.164, N.165, K.188, A.190, T.191, F.237, T.238, G.239, S.240, T.243, E.263, A.264, D.265, C.302, E.402, F.404, L.430, H.479 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.238 Hydrogen bonds: B:N.162, B:F.164, B:T.191, B:S.240, B:E.263 Salt bridges: B:R.27, B:K.188 NAP.5: 22 residues within 4Å: Chain C: R.27, I.161, N.162, A.163, F.164, N.165, K.188, 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:T.238 Hydrogen bonds: C:N.162, C:K.188, C:T.191, C:S.240, C:T.243, C:E.263 Salt bridges: C:R.27, C:K.188 NAP.7: 23 residues within 4Å: Chain D: R.27, I.161, N.162, A.163, F.164, N.165, K.188, 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 9 PLIP interactions: 9 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: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 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:T.238 Hydrogen bonds: E:N.162, E:T.191, E:T.191, E:S.240, E:T.243, E:E.263 Salt bridges: E:R.27, E:K.188 NAP.11: 23 residues within 4Å: Chain F: R.27, I.161, N.162, A.163, F.164, N.165, K.188, 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 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:T.238 Hydrogen bonds: F:N.162, F:F.164, F:T.191, F:S.240, F:E.263, F:E.402 Salt bridges: F:R.27, F:K.188

6 x COO: CROTONYL COENZYME A(Non-covalent)

COO.2: 15 residues within 4Å: Chain A: K.76, V.105, G.109, F.115, T.116, S.119, F.166, W.169, S.472, P.473, L.474, Q.476, R.646 Chain B: P.138, L.139 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:P.138, A:K.76, A:T.116, A:S.119, A:Q.476 Hydrophobic interactions: A:V.105, A:F.166, A:W.169 Salt bridges: A:K.76, A:R.646 pi-Stacking: A:F.115, A:F.115 COO.4: 15 residues within 4Å: Chain A: P.138, L.139 Chain B: K.76, L.83, V.105, G.109, F.115, T.116, S.119, F.166, W.169, S.472, P.473, L.474, R.646 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.105, B:F.166, B:W.169 Hydrogen bonds: B:K.76, B:T.116, B:S.119, B:R.646, A:P.138 Salt bridges: B:R.646 pi-Stacking: B:F.115, B:F.115 COO.6: 16 residues within 4Å: Chain C: K.76, L.83, W.104, V.105, G.109, F.115, T.116, S.119, F.166, W.169, S.472, P.473, L.474, R.646 Chain D: P.138, L.139 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.105, C:F.166, C:W.169 Hydrogen bonds: C:K.76, C:T.116, C:S.119, C:R.646, D:P.138 Salt bridges: C:K.76, C:R.646 pi-Stacking: C:F.115, C:F.115 COO.8: 13 residues within 4Å: Chain C: P.138, L.139 Chain D: K.76, W.104, V.105, F.115, T.116, S.119, F.166, W.169, P.473, L.474, R.646 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.105, D:F.166, D:W.169 Hydrogen bonds: D:K.76, D:T.116, D:S.119, C:P.138 Salt bridges: D:R.646 pi-Stacking: D:F.115, D:F.115 COO.10: 16 residues within 4Å: Chain E: K.76, L.83, V.105, G.109, F.115, T.116, S.119, F.166, W.169, S.472, P.473, L.474, Q.476, R.646 Chain F: P.138, L.139 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:V.105, E:F.166, E:W.169 Hydrogen bonds: E:K.76, E:T.116, E:T.116, E:S.119, E:Q.476, E:R.646, F:P.138 Salt bridges: E:K.76, E:R.646 pi-Stacking: E:F.115, E:F.115 COO.12: 13 residues within 4Å: Chain E: P.138, L.139 Chain F: K.76, V.105, G.109, F.115, T.116, S.119, F.166, W.169, P.473, L.474, R.646 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.105, F:F.166, F:W.169 Hydrogen bonds: F:K.76, F:T.116, F:S.119 Salt bridges: F:R.646 pi-Stacking: F:F.115, F:F.115

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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