SMTL ID : 9n4y.1

CryoEM structure of a filamentous soluble pyridine nucleotide transhydrogenase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.70 Å

Oligo State

homo-14-mer

Ligands

14 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 34 residues within 4Å: Chain A: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, S.147, I.186, E.189, Y.190, N.273, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 Chain E: Y.445, P.446 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.186, A:Y.190 Hydrogen bonds: A:G.14, A:A.16, A:D.36, A:R.37, A:R.37, A:N.43, A:N.43, A:C.44, A:T.49, A:T.49, A:A.116, A:A.116, A:S.147, A:D.310, A:S.316, A:A.318, A:S.319, E:Y.445 FAD.2: 37 residues within 4Å: Chain B: G.12, T.13, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, G.114, T.115, A.116, A.144, T.145, G.146, S.147, I.186, E.189, Y.190, R.270, N.273, L.277, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 Chain H: Y.445 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:I.186, B:Y.190 Hydrogen bonds: B:T.13, B:A.16, B:D.36, B:R.37, B:N.43, B:N.43, B:C.44, B:K.53, B:A.116, B:A.116, B:S.147, B:D.310, B:S.316, B:A.318, B:S.319, H:Y.445 FAD.3: 35 residues within 4Å: Chain C: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, G.114, A.116, A.144, T.145, G.146, I.186, E.189, Y.190, R.270, L.277, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 Chain D: Y.445, P.446 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.186, C:I.186, C:Y.190 Hydrogen bonds: C:G.14, C:A.16, C:D.36, C:R.37, C:N.43, C:C.44, C:K.53, C:A.116, C:A.116, C:G.146, C:D.310, C:S.316, C:A.318, C:S.319, D:Y.445 FAD.4: 33 residues within 4Å: Chain C: Y.445 Chain D: I.11, G.12, T.13, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, T.115, A.116, A.144, T.145, G.146, I.186, Y.190, R.270, K.276, G.309, D.310, S.316, L.317, A.318, S.319, A.321 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.186, D:Y.190 Hydrogen bonds: D:T.13, D:T.13, D:A.16, D:D.36, D:R.37, D:N.43, D:N.43, D:K.53, D:A.116, D:S.147, D:D.310, D:S.316, D:A.318, D:S.319, C:Y.445 FAD.5: 34 residues within 4Å: Chain A: Y.445, P.446 Chain E: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, I.186, E.189, Y.190, R.270, N.273, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.186, E:Y.190 Hydrogen bonds: E:A.16, E:D.36, E:R.37, E:N.43, E:N.43, E:C.44, E:T.49, E:K.53, E:A.116, E:A.116, E:D.310, E:S.316, E:A.318, E:S.319, A:Y.445 FAD.6: 37 residues within 4Å: Chain F: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, G.114, A.116, A.144, T.145, G.146, S.147, I.186, E.189, Y.190, R.270, N.273, L.277, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 Chain G: Y.445, P.446 20 PLIP interactions: 19 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:I.186, F:Y.190 Hydrogen bonds: F:G.14, F:A.16, F:D.36, F:R.37, F:N.43, F:N.43, F:C.44, F:T.49, F:T.49, F:K.53, F:A.116, F:A.116, F:S.147, F:D.310, F:S.316, F:A.318, F:S.319, G:Y.445 FAD.7: 34 residues within 4Å: Chain F: Y.445 Chain G: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, S.147, I.186, E.189, Y.190, R.270, N.273, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 20 PLIP interactions: 19 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:I.186, G:I.186, G:Y.190 Hydrogen bonds: G:G.14, G:A.16, G:D.36, G:D.36, G:R.37, G:N.43, G:N.43, G:C.44, G:K.53, G:A.116, G:S.147, G:N.273, G:D.310, G:S.316, G:A.318, G:S.319, F:Y.445 FAD.8: 34 residues within 4Å: Chain B: Y.445 Chain H: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, I.186, E.189, Y.190, R.270, N.273, K.276, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 18 PLIP interactions: 17 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: H:I.186, H:Y.190 Hydrogen bonds: H:A.16, H:D.36, H:R.37, H:N.43, H:N.43, H:N.43, H:C.44, H:K.53, H:A.116, H:A.116, H:N.273, H:D.310, H:S.316, H:A.318, H:S.319, B:Y.445 FAD.9: 35 residues within 4Å: Chain I: G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, G.114, T.115, A.116, A.144, T.145, G.146, I.186, E.189, Y.190, R.270, N.273, K.276, L.277, D.310, S.316, L.317, A.318, S.319, A.321 Chain J: Y.445, P.446 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:I.186, I:Y.190 Hydrogen bonds: I:A.16, I:D.36, I:R.37, I:N.43, I:N.43, I:N.43, I:C.44, I:K.53, I:A.116, I:A.116, I:K.276, I:D.310, I:S.316, I:A.318, I:S.319, J:Y.445 FAD.10: 33 residues within 4Å: Chain I: Y.445 Chain J: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, S.147, S.165, I.186, Y.190, R.270, N.273, G.309, D.310, S.316, L.317, A.318, S.319, A.321 18 PLIP interactions: 17 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.186, J:Y.190 Hydrogen bonds: J:G.14, J:A.16, J:D.36, J:R.37, J:N.43, J:N.43, J:C.44, J:K.53, J:A.116, J:A.116, J:S.147, J:D.310, J:S.316, J:A.318, J:S.319, I:Y.445 FAD.11: 33 residues within 4Å: Chain K: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, L.47, G.48, T.49, S.52, A.116, A.144, T.145, G.146, S.147, S.165, I.186, E.189, Y.190, R.270, N.273, G.309, D.310, S.316, L.317, A.318, A.321, Y.349 18 PLIP interactions: 18 interactions with chain K Hydrophobic interactions: K:I.186, K:I.186, K:Y.190 Hydrogen bonds: K:T.13, K:G.14, K:A.16, K:D.36, K:N.43, K:N.43, K:N.43, K:C.44, K:S.52, K:A.116, K:A.116, K:S.147, K:D.310, K:S.316, K:A.318 FAD.12: 32 residues within 4Å: Chain L: I.11, G.12, G.14, P.15, A.16, V.34, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, A.116, A.144, T.145, G.146, S.147, I.186, Y.190, R.270, N.273, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 19 PLIP interactions: 19 interactions with chain L Hydrophobic interactions: L:I.186, L:I.186, L:Y.190 Hydrogen bonds: L:A.16, L:D.36, L:D.36, L:R.37, L:N.43, L:N.43, L:C.44, L:T.49, L:T.49, L:A.116, L:A.116, L:S.147, L:D.310, L:S.316, L:A.318, L:S.319 FAD.13: 32 residues within 4Å: Chain M: I.11, G.12, G.14, P.15, A.16, V.34, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, I.186, R.270, N.273, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 Chain N: Y.445 20 PLIP interactions: 19 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:I.186 Hydrogen bonds: M:G.14, M:A.16, M:D.36, M:R.37, M:N.43, M:N.43, M:C.44, M:T.49, M:T.49, M:K.53, M:A.116, M:A.116, M:S.147, M:D.310, M:D.310, M:S.316, M:A.318, M:S.319, N:Y.445 FAD.14: 34 residues within 4Å: Chain M: Y.445, P.446 Chain N: I.11, G.12, G.14, P.15, A.16, D.35, D.36, R.37, G.42, N.43, C.44, G.48, T.49, S.52, K.53, A.116, A.144, T.145, G.146, I.186, Y.190, R.270, N.273, L.277, G.309, D.310, S.316, L.317, A.318, S.319, A.321, Y.349 18 PLIP interactions: 17 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:I.186, N:Y.190 Hydrogen bonds: N:G.14, N:A.16, N:D.36, N:R.37, N:R.37, N:N.43, N:C.44, N:K.53, N:A.116, N:A.116, N:G.146, N:D.310, N:S.316, N:A.318, N:S.319, M:Y.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y. et al., CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes. Structure (2025)

Release Date

2025-07-16

Peptides

Soluble pyridine nucleotide transhydrogenase: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
d

C
g

D
j

E
m

F
p

G
s

H
v

I
y

J
b

K
e

L
h

M
k

N
n

Soluble pyridine nucleotide transhydrogenase