SMTL ID : 8jwk.2 (1 other biounit)

The second purified state crystal structure of AKRtyl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-octamer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 5 residues within 4Å: Chain A: W.117, H.120 Chain G: D.95, D.98, K.99 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.95, G:K.99

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 28 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, S.259, G.260, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 Chain E: W.351 22 PLIP interactions: 22 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:S.180, B:N.181, B:Q.206, B:S.235, B:L.237, B:G.239, B:G.240, B:G.260, B:G.309, B:Q.315, B:S.318, B:S.318 Water bridges: B:S.235, B:G.309 Salt bridges: B:R.311 NDP.3: 29 residues within 4Å: 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, R.255, R.256, A.257, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 Chain G: W.351 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:R.256, D:A.257, D:G.309, D:Q.315, D:S.318, D:S.318 Water bridges: D:N.42, D:S.235, D:K.248, D:K.248, D:G.309 Salt bridges: D:R.256, D:R.311 NDP.4: 24 residues within 4Å: Chain C: W.351 Chain F: G.39, T.40, M.41, N.42, D.68, Y.73, H.150, S.180, N.181, Q.206, W.234, S.235, P.236, L.237, H.238, G.239, G.290, I.307, G.309, R.311, Q.315, S.318, A.319 18 PLIP interactions: 18 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.309, F:Q.315, F:S.318, F:S.318 Salt bridges: F:R.311 NDP.5: 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, K.248, 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 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:R.256, H:A.257, H:G.309, H:Q.315, H:S.318, H:S.318 Water bridges: H:G.309, H:G.309 Salt bridges: H:K.248, H:R.256, H:R.256, H:R.311

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
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

Aldo/keto reductase

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