SMTL ID : 8pin.1

Crystal structure of Ser33

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

homo-tetramer

Ligands

3 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Poli-ALA(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 7 residues within 4Å: Chain A: E.309 Chain B: W.149, R.152, G.153, K.232, D.233, G.234 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.232 Hydrogen bonds: B:D.233, A:E.309, A:E.309 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.2: 10 residues within 4Å: Chain A: M.188 Chain C: R.147, W.149, R.152, G.153, D.207, K.232, D.233, G.234 Chain D: E.309 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.149 Hydrogen bonds: C:R.147, D:E.309, D:E.309 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.3: 8 residues within 4Å: Chain C: E.309 Chain D: W.149, K.154, N.204, D.207, A.230, K.232, D.233 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:E.309, D:K.232 Hydrogen bonds: D:D.233, D:D.233, D:D.233, D:D.233

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

NAD.4: 23 residues within 4Å: Chain A: F.108, N.110, V.114, I.159, Y.161, G.162, H.163, I.164, Y.182, D.183, I.184, I.187, H.212, V.213, P.214, T.219, M.222, A.240, S.241, R.242, D.266, H.302, G.304 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.110, A:V.114 Hydrogen bonds: A:H.163, A:I.164, A:I.184, A:V.213, A:R.242, A:D.266, A:G.304 Salt bridges: A:H.163 NAD.6: 22 residues within 4Å: Chain B: F.108, N.110, V.114, G.160, G.162, H.163, I.164, Y.182, D.183, I.184, H.212, V.213, P.214, T.219, M.222, A.240, S.241, R.242, D.266, H.302, G.304, G.305 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.110, B:V.114, B:I.164 Hydrogen bonds: B:H.163, B:I.164, B:V.213, B:A.240, B:R.242, B:D.266, B:G.304, B:G.305 Salt bridges: B:H.163 NAD.8: 24 residues within 4Å: Chain C: F.108, N.110, V.114, G.160, Y.161, G.162, H.163, I.164, Y.182, D.183, I.184, I.187, H.212, V.213, P.214, T.219, M.222, A.240, S.241, R.242, D.266, H.302, G.304, G.305 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:N.110 Hydrogen bonds: C:Y.161, C:Y.161, C:H.163, C:H.163, C:I.164, C:I.184, C:V.213, C:R.242, C:D.266, C:D.266, C:G.304 Salt bridges: C:H.163 NAD.10: 23 residues within 4Å: Chain D: F.108, N.110, V.114, I.159, G.160, Y.161, G.162, H.163, I.164, D.183, I.184, H.212, V.213, P.214, T.219, M.222, A.240, S.241, R.242, D.266, H.302, G.304, G.305 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:N.110, D:V.114 Hydrogen bonds: D:Y.161, D:H.163, D:I.164, D:I.184, D:V.213, D:R.242, D:D.266, D:G.304, D:G.305 Salt bridges: D:H.163, D:H.163

4 x PI: HYDROGENPHOSPHATE ION(Non-covalent)

PI.5: 9 residues within 4Å: Chain A: H.359, N.361, V.362, P.363, G.364, V.365, L.366 Chain D: N.377, I.378 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:N.377, D:I.378, A:N.361, A:V.362, A:G.364, A:V.365, A:L.366 PI.7: 8 residues within 4Å: Chain B: H.359, N.361, V.362, G.364, V.365, L.366 Chain C: N.377, I.378 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.361, B:V.362, B:G.364, B:V.365, B:L.366, C:I.378, C:I.378 PI.9: 9 residues within 4Å: Chain B: N.377, I.378 Chain C: H.359, N.361, V.362, P.363, G.364, V.365, L.366 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:V.365, C:L.366, B:I.378, B:I.378 PI.11: 9 residues within 4Å: Chain A: N.377, I.378 Chain D: H.359, N.361, V.362, P.363, G.364, V.365, L.366 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.359, D:V.365, D:L.366, A:I.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perrone, S. et al., Crystal structure of Ser33. To Be Published

Release Date

2025-01-15

Peptides

D-3-phosphoglycerate dehydrogenase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

D-3-phosphoglycerate dehydrogenase 2