SMTL ID : 8jwm.1

Crystal structure of AKRtyl-NADP-tylosin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-octamer

Ligands

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

NAP.1: 30 residues within 4Å: Chain A: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 Chain H: W.351 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.234, A:W.234 Hydrogen bonds: A:T.40, A:M.41, A:N.42, A:D.68, A:D.68, A:Y.73, A:S.180, A:N.181, A:Q.206, A:S.235, A:L.237, A:G.239, A:G.240, A:R.256, A:A.257, A:G.309, A:G.309, A:Q.315, A:S.318, A:S.318 Water bridges: A:N.42, A:S.235, A:K.248, A:K.248, A:K.248, A:R.255, A:R.311 Salt bridges: A:R.256, A:R.311 NAP.3: 31 residues within 4Å: Chain B: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 Chain F: W.351 Ligands: TYK.5 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:W.234, B:W.234 Hydrogen bonds: B:T.40, B:M.41, B:N.42, B:D.68, B:D.68, B:Y.73, B:S.180, B:N.181, B:Q.206, B:S.235, B:L.237, B:G.239, B:G.240, B:R.256, B:R.256, B:A.257, B:G.309, B:G.309, B:Q.315, B:S.318, B:S.318 Water bridges: B:N.42, B:K.248, B:R.255, B:R.256, B:G.290, B:R.311 Salt bridges: B:R.256, B:R.311 NAP.6: 30 residues within 4Å: Chain C: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 Chain D: W.351 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:W.234, C:W.234 Hydrogen bonds: C:T.40, C:M.41, C:N.42, C:D.68, C:Y.73, C:S.180, C:N.181, C:Q.206, C:S.235, C:L.237, C:G.239, C:G.240, C:R.256, C:A.257, C:G.309, C:G.309, C:Q.315, C:S.318, C:S.318 Water bridges: C:N.42, C:K.248, C:K.248, C:R.255, C:R.256, C:G.290, C:R.311 Salt bridges: C:R.256, C:R.311 NAP.8: 30 residues within 4Å: Chain C: W.351 Chain D: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:W.234, D:W.234 Hydrogen bonds: D:T.40, D:M.41, D:N.42, D:D.68, D:S.180, D:N.181, D:Q.206, D:S.235, D:L.237, D:G.239, D:G.240, D:R.256, D:A.257, D:G.309, D:G.309, D:Q.315, D:S.318, D:S.318 Water bridges: D:N.42, D:S.235, D:K.248, D:R.255, D:R.311 Salt bridges: D:R.256, D:R.311 NAP.9: 30 residues within 4Å: Chain E: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 Chain G: W.351 33 PLIP interactions: 33 interactions with chain E Hydrophobic interactions: E:W.234, E:W.234 Hydrogen bonds: E:T.40, E:M.41, E:N.42, E:D.68, E:Y.73, E:S.180, E:N.181, E:Q.206, E:S.235, E:L.237, E:G.239, E:G.240, E:R.256, E:A.257, E:G.309, E:G.309, E:Q.315, E:S.318, E:S.318 Water bridges: E:N.42, E:K.248, E:K.248, E:R.255, E:R.256, E:G.290, E:G.290, E:R.311, E:R.311 Salt bridges: E:R.256, E:R.256, E:R.311 NAP.11: 33 residues within 4Å: Chain B: W.351 Chain F: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, K.248, N.254, R.255, R.256, A.257, G.290, I.307, V.308, G.309, R.311, Q.315, S.318, A.319 33 PLIP interactions: 33 interactions with chain F Hydrophobic interactions: F:W.234, F:W.234 Hydrogen bonds: F:T.40, F:M.41, F:N.42, F:D.68, F:D.68, F:S.180, F:N.181, F:Q.206, F:S.235, F:L.237, F:G.239, F:G.240, F:K.248, F:R.255, F:R.256, F:A.257, F:G.309, F:G.309, F:Q.315, F:S.318, F:S.318 Water bridges: F:N.42, F:S.235, F:G.243, F:K.248, F:G.253, F:R.311, F:R.311 Salt bridges: F:K.248, F:R.256, F:R.311 NAP.13: 31 residues within 4Å: Chain E: W.351 Chain G: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, K.248, N.254, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318 32 PLIP interactions: 32 interactions with chain G Hydrophobic interactions: G:W.234, G:W.234 Hydrogen bonds: G:T.40, G:M.41, G:N.42, G:N.42, G:D.68, G:S.180, G:N.181, G:Q.206, G:S.235, G:L.237, G:G.239, G:G.240, G:K.248, G:R.255, G:R.256, G:A.257, G:G.309, G:Q.315, G:S.318, G:S.318 Water bridges: G:N.42, G:G.243, G:K.248, G:R.256, G:G.290, G:R.311, G:R.311 Salt bridges: G:K.248, G:R.256, G:R.311 NAP.15: 30 residues within 4Å: Chain A: W.351 Chain H: G.39, T.40, M.41, N.42, D.68, Y.73, K.105, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.240, G.243, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 30 PLIP interactions: 30 interactions with chain H Hydrophobic interactions: H:W.234, H:W.234 Hydrogen bonds: H:T.40, H:M.41, H:N.42, H:D.68, H:D.68, H:S.180, H:N.181, H:Q.206, H:S.235, H:L.237, H:G.239, H:G.240, H:R.256, H:A.257, H:G.309, H:G.309, H:Q.315, H:S.318, H:S.318 Water bridges: H:N.42, H:S.235, H:K.248, H:R.255, H:G.290, H:R.311, H:R.311 Salt bridges: H:R.256, H:R.311

7 x TYK: TYLOSIN(Non-covalent)

TYK.2: 12 residues within 4Å: Chain A: C.212, E.213, R.215, Q.270, Q.271, E.273, Q.274, R.277, L.281, E.337, I.338, P.340 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.270, A:Q.271, A:L.281, A:E.337, A:I.338, A:I.338, A:P.340 Hydrogen bonds: A:E.213, A:R.215, A:R.277, A:R.277 Water bridges: A:C.212, A:R.214, A:Q.274, A:D.280 Salt bridges: A:R.277 TYK.4: 11 residues within 4Å: Chain B: C.212, E.213, R.215, Q.270, Q.271, E.273, Q.274, R.277, E.337, I.338, P.340 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Q.271, B:E.337, B:I.338, B:P.340 Hydrogen bonds: B:E.213, B:R.215, B:Q.274, B:R.277, B:K.284, B:K.284 Water bridges: B:C.212, B:R.214, B:Q.271, B:Q.274, B:R.277 Salt bridges: B:R.277 TYK.5: 9 residues within 4Å: Chain B: M.41, Y.73, W.75, H.150, S.259, G.260, R.261 Chain F: W.351 Ligands: NAP.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:W.75, B:R.261, F:W.351, F:W.351 Hydrogen bonds: B:W.75 Water bridges: B:R.261 Salt bridges: B:R.261 TYK.7: 12 residues within 4Å: Chain C: C.212, E.213, R.215, Q.270, Q.271, E.273, Q.274, R.277, L.281, E.337, I.338, P.340 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Q.270, C:Q.270, C:Q.271, C:L.281, C:E.337, C:I.338, C:P.340 Hydrogen bonds: C:E.213, C:R.215, C:E.273, C:Q.274, C:R.277, C:R.277 Water bridges: C:C.212, C:R.214, C:Q.274 Salt bridges: C:R.277 TYK.10: 11 residues within 4Å: Chain E: C.212, E.213, R.215, Q.270, Q.271, E.273, Q.274, R.277, E.337, I.338, P.340 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Q.270, E:Q.271, E:E.337, E:P.340 Hydrogen bonds: E:E.213, E:R.215, E:E.273, E:Q.274 Water bridges: E:C.212, E:R.214, E:Q.274 Salt bridges: E:R.277, E:R.277 TYK.12: 11 residues within 4Å: Chain F: C.212, E.213, R.215, Q.270, Q.271, E.273, Q.274, R.277, E.337, I.338, P.340 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:Q.270, F:Q.271, F:E.337, F:I.338, F:P.340 Hydrogen bonds: F:E.213, F:R.215, F:Q.274, F:R.277, F:R.277 Water bridges: F:C.212, F:R.214, F:Q.274 Salt bridges: F:R.277 TYK.14: 13 residues within 4Å: Chain G: C.212, E.213, R.215, Q.270, Q.271, E.273, Q.274, R.277, D.280, L.281, E.337, I.338, P.340 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:Q.271, G:L.281, G:E.337, G:I.338, G:P.340 Hydrogen bonds: G:E.213, G:R.215, G:E.273, G:Q.274, G:R.277, G:R.277 Water bridges: G:C.212, G:R.214, G:Q.274, G:D.280 Salt bridges: G:R.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, Z. et al., A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D. Nat Commun (2024)

Release Date

2024-04-10

Peptides

Aldo/keto reductase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Aldo/keto reductase

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