SMTL ID : 7byi.1

Structure of SHMT2 in complex with CBX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-1-1-mer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: S.121, G.122, S.123, H.150, T.256, H.258 Chain B: Y.75, Y.120, G.304, G.305 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.122, A:S.123, A:S.123, B:Y.75, B:Y.75, B:Y.120, B:G.304, B:G.305 Salt bridges: A:H.258, A:K.259 PO4.5: 11 residues within 4Å: Chain A: Y.75, Y.120, G.304, G.305 Chain B: S.121, G.122, S.123, H.150, T.256, H.258, K.259 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.75, A:Y.75, A:Y.120, A:G.305, B:G.122, B:S.123 Salt bridges: B:H.258, B:K.259

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

PEG.2: 1 residues within 4Å: Chain A: K.438 No protein-ligand interaction detected (PLIP)

2 x CBO: CARBENOXOLONE(Non-covalent)

CBO.3: 11 residues within 4Å: Chain A: L.145, L.151, I.162, S.205, H.233, R.404 Chain B: E.77, Y.84, Y.85, F.299, P.300 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.84, B:Y.84, B:F.299, B:P.300, A:L.145, A:L.145, A:L.151, A:I.162 Hydrogen bonds: B:Y.85 Salt bridges: A:R.404 CBO.4: 8 residues within 4Å: Chain A: E.77, Y.84 Chain B: L.145, H.150, L.151, Y.155, S.157, I.162 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.145, B:L.151, B:I.162 Hydrogen bonds: B:L.151 Salt bridges: B:H.150, B:K.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Structure of SHMT2 with CBX. To Be Published

Release Date

2021-09-15

Peptides

Serine hydroxymethyltransferase, mitochondrial: A
Serine hydroxymethyltransferase, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase, mitochondrial

Serine hydroxymethyltransferase, mitochondrial