SMTL ID : 8uxu.1

Cryo-EM structure of a bacterial nitrilase filament with a covalent adduct derived from benzonitrile hydrolysis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x HBX: benzaldehyde(Covalent)

HBX.1: 13 residues within 4Å: Chain A: E.48, Y.54, W.59, M.114, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.59, A:T.135, A:L.194 Hydrogen bonds: A:K.131, A:T.135 pi-Stacking: A:W.166, A:F.202 HBX.2: 12 residues within 4Å: Chain B: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.59, B:T.135, B:L.194 Hydrogen bonds: B:Y.54 pi-Stacking: B:W.166, B:F.202 HBX.3: 12 residues within 4Å: Chain C: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.59, C:T.135, C:W.166, C:P.190, C:L.194 Hydrogen bonds: C:W.166 pi-Stacking: C:F.202 HBX.4: 11 residues within 4Å: Chain D: Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.59, D:T.135, D:W.166, D:L.194 Hydrogen bonds: D:Y.54 pi-Stacking: D:W.166, D:F.202 HBX.5: 12 residues within 4Å: Chain E: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:W.59, E:T.135, E:L.194 pi-Stacking: E:W.166, E:F.202 HBX.6: 12 residues within 4Å: Chain F: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:W.59, F:T.135, F:L.194 Hydrogen bonds: F:K.131 pi-Stacking: F:W.166, F:W.166, F:F.202 HBX.7: 12 residues within 4Å: Chain G: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:W.59, G:T.135, G:L.194 Hydrogen bonds: G:K.131 pi-Stacking: G:W.166, G:F.202 HBX.8: 11 residues within 4Å: Chain H: Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:W.59, H:T.135, H:P.190, H:L.194 Hydrogen bonds: H:K.131 pi-Stacking: H:W.166, H:F.202 HBX.9: 12 residues within 4Å: Chain I: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:W.59, I:T.135, I:L.194 Hydrogen bonds: I:K.131 pi-Stacking: I:W.166, I:F.202 HBX.10: 12 residues within 4Å: Chain J: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:W.59, J:T.135 Hydrogen bonds: J:K.131 pi-Stacking: J:W.166, J:F.202 HBX.11: 13 residues within 4Å: Chain K: E.48, Y.54, W.59, M.114, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:W.59, K:T.135, K:L.194 Hydrogen bonds: K:K.131 pi-Stacking: K:W.166, K:F.202 HBX.12: 12 residues within 4Å: Chain L: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:W.59, L:T.135 pi-Stacking: L:W.166, L:F.202 HBX.13: 12 residues within 4Å: Chain M: E.48, Y.54, W.59, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:W.59, M:T.135, M:L.194 pi-Stacking: M:W.166, M:F.202 HBX.14: 13 residues within 4Å: Chain N: E.48, Y.54, W.59, M.114, K.131, T.135, E.138, C.165, W.166, P.190, M.192, L.194, F.202 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:W.59, N:T.135, N:P.190, N:L.194 pi-Stacking: N:W.166, N:F.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aguirre-Sampieri, S. et al., Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis. J.Struct.Biol. (2024)

Release Date

2024-05-01

Peptides

Nitrilase: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Nitrilase