SMTL ID : 7xzp.1

Formate-tetrahydrofolate ligase in complex with berberine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

4 x BER: BERBERINE(Non-covalent)

BER.1: 2 residues within 4Å: Chain A: Y.233 Ligands: BER.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.233 pi-Stacking: A:Y.233, A:Y.233 BER.2: 10 residues within 4Å: Chain A: V.153, Y.154, Q.155, T.156, N.157, P.163, V.193, Y.233 Ligands: BER.1, PRO.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.163 BER.9: 8 residues within 4Å: Chain B: E.74, G.75, T.78, N.385, R.386, F.387, P.388, W.415 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.387, B:F.387, B:P.388, B:W.415, B:W.415, B:W.415 pi-Stacking: B:W.415, B:W.415, B:W.415 BER.10: 6 residues within 4Å: Chain B: Q.374, K.377, E.403, E.404, L.405, G.406 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.374

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: K.76, R.99, G.305, F.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.306 Salt bridges: A:K.76, A:R.99 SO4.11: 5 residues within 4Å: Chain B: K.76, R.99, E.303, G.305, F.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.306 Salt bridges: B:K.76, B:R.99

9 x PRO: PROLINE(Non-covalent)

PRO.4: 3 residues within 4Å: Chain A: K.221, R.241, H.246 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.241, P.4 Salt bridges: A:K.221, A:R.241, A:H.246 PRO.5: 3 residues within 4Å: Chain A: K.188, K.189, V.190 3 PLIP interactions: 3 interactions with chain A, Hydrogen bonds: A:K.189, A:V.190 Salt bridges: A:K.188 PRO.6: 6 residues within 4Å: Chain A: A.14, Q.15, V.122, P.123, M.124, E.125 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:E.125 Hydrogen bonds: A:A.14, A:M.124, A:E.125 PRO.7: 6 residues within 4Å: Chain A: R.177, R.180, M.536, G.540 Chain B: Y.154, V.190 8 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.177, A:G.540, B:Y.154, B:Y.154, P.7 Salt bridges: A:R.177, A:R.180 Hydrophobic interactions: B:V.190 PRO.8: 3 residues within 4Å: Chain A: Y.154, Q.155 Ligands: BER.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.154 Hydrogen bonds: A:Q.155, P.8, P.8, P.8 PRO.12: 4 residues within 4Å: Chain B: K.221, E.222, R.241, H.246 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B Hydrogen bonds: P.12, B:H.246 Hydrophobic interactions: B:E.222 Salt bridges: B:R.241, B:H.246 PRO.13: 5 residues within 4Å: Chain A: Y.154, V.190 Chain B: R.177, R.180, M.536 7 PLIP interactions: 2 interactions with chain B, 4 Ligand-Ligand interactions, 1 interactions with chain A Salt bridges: B:R.177, B:R.180 Hydrogen bonds: P.13, P.13, P.13, P.13 Hydrophobic interactions: A:V.190 PRO.14: 3 residues within 4Å: Chain B: F.440, E.441, Y.442 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: P.14, P.14, B:F.440, B:F.440, B:Y.442 PRO.15: 5 residues within 4Å: Chain B: G.59, M.294, I.325, R.326, D.328 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:I.325 Hydrogen bonds: B:R.326, B:R.326, P.15, P.15 Salt bridges: B:R.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, J. et al., Identification of FtfL as a novel target of berberine in intestinal bacteria. Bmc Biol. (2023)

Release Date

2023-06-07

Peptides

Formate--tetrahydrofolate ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formate--tetrahydrofolate ligase

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