SMTL ID : 9l3e.1

Structure of GAPDH complexed with Leu-F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

1 x 01: (4~{a}~{S},5~{S},5~{a}~{R},6~{S},8~{a}~{R},9~{S},9~{a}~{S})-3,6,9-trimethyl-5-[(1~{S},2~{R})-2-methyl-4-(3-methylfuran-2-yl)-1-oxidanyl-butyl]-3,4,5~{a},6,7,8,8~{a},9-octahydro-2~{H}-cyclopenta[g]chromene-4~{a},5,9~{a}-triol

01.1: 17 residues within 4Å: Chain A: I.15, S.123, A.124, P.125, S.152, C.153, T.154, T.178, H.180, T.183, T.212, A.214, R.235, N.317, E.318, Y.321 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.15, A:T.154, A:T.183, A:T.212, A:A.214, A:N.317 Hydrogen bonds: A:N.317

7 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: H.280 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.280 ZN.3: 1 residues within 4Å: Chain A: H.331 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.331 ZN.8: 1 residues within 4Å: Chain B: H.307 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.307 ZN.9: 1 residues within 4Å: Chain B: H.331 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.331, H2O.8, H2O.9 ZN.14: 1 residues within 4Å: Chain C: H.307 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.307, H2O.26 ZN.20: 1 residues within 4Å: Chain D: H.58 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.58 ZN.21: 1 residues within 4Å: Chain D: H.331 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.331

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: H.58 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: H.307 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: H.58 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain C: H.58 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: P.253, H.307 Ligand excluded by PLIP

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 20 residues within 4Å: Chain A: N.10, G.11, F.12, G.13, R.14, I.15, N.35, D.36, P.37, F.38, T.100, G.101, F.103, T.104, S.123, A.124, P.125, A.184 Chain C: P.192 Ligands: 01.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.104 Hydrogen bonds: A:G.13, A:R.14, A:I.15, A:N.35, A:R.81, A:P.125 Water bridges: A:G.16, A:R.17, A:G.101 pi-Stacking: A:F.38 NAD.11: 25 residues within 4Å: Chain B: N.10, G.11, F.12, G.13, R.14, I.15, N.35, D.36, P.37, F.38, I.39, E.80, R.81, S.99, T.100, G.101, F.103, S.123, A.124, C.153, T.183, A.184, N.317, Y.321 Chain D: P.192 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.15, B:I.15, B:Y.321 Hydrogen bonds: B:F.12, B:F.12, B:R.14, B:I.15, B:N.35, B:R.81, B:N.317, B:N.317 Water bridges: B:N.10, B:N.10, B:F.12, B:G.13, B:G.16, B:R.17, B:G.101, B:S.123, B:A.184, B:A.184 pi-Stacking: B:F.38 NAD.16: 24 residues within 4Å: Chain A: P.192 Chain C: N.10, G.11, F.12, G.13, R.14, I.15, N.35, D.36, P.37, F.38, I.39, E.80, R.81, S.99, T.100, G.101, F.103, S.123, A.124, C.153, A.184, N.317, Y.321 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.15, C:I.15, C:Y.321 Hydrogen bonds: C:F.12, C:F.12, C:R.14, C:I.15, C:N.35, C:R.81, C:N.317, C:N.317 Water bridges: C:N.10, C:N.10, C:G.13, C:G.16, C:R.17, C:G.101, C:S.123, C:A.184, C:A.184 pi-Stacking: C:F.38 NAD.23: 19 residues within 4Å: Chain B: P.192 Chain D: N.10, G.11, F.12, G.13, R.14, I.15, N.35, D.36, P.37, F.38, I.39, S.99, T.100, G.101, S.123, A.124, P.125, A.184 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:F.12, D:R.14, D:I.15, D:T.100, D:P.125 Water bridges: D:G.16, D:R.17, D:R.17

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: D.167, N.168, F.169, E.251, K.252 No protein-ligand interaction detected (PLIP) PEG.12: 1 residues within 4Å: Chain B: H.280 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.278, B:H.280 PEG.18: 5 residues within 4Å: Chain C: L.304, N.305 Chain D: V.172, E.173, G.227 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.305, D:E.173, D:E.173 PEG.19: 6 residues within 4Å: Chain C: D.167, N.168, F.169, G.170, E.251, K.252 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.251, C:K.252 PEG.24: 6 residues within 4Å: Chain D: A.129, P.130, M.131, F.132, K.140, K.220 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.140 PEG.25: 5 residues within 4Å: Chain D: D.167, N.168, F.169, G.170, K.252 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.252

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 9 residues within 4Å: Chain B: D.128, A.129, P.130, M.131, F.132, N.137, K.140, L.145, K.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.128, B:M.131, B:N.137 PG4.17: 9 residues within 4Å: Chain C: D.128, A.129, P.130, M.131, F.132, N.137, K.140, L.145, K.220 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.131

Links

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Citation

Zhou, T.T. et al., Plant defense-directed discovery of a natural anti-psoriasis agent targeting GAPDH. Sci Adv (2025)

Release Date

2025-08-06

Peptides

Glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
R

D
Q

Glyceraldehyde-3-phosphate dehydrogenase