SMTL ID : 8x8j.1

The structure of AbBioc in complex with inhibitor sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 19 residues within 4Å: Chain A: C.30, E.50, G.52, C.53, G.54, N.57, L.58, N.74, D.75, L.76, Y.77, G.95, D.96, V.97, G.112, S.113, A.114, W.117, M.118 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.52, A:N.57, A:L.58, A:L.76, A:D.96, A:D.96, A:V.97, A:S.113 Water bridges: A:S.55, A:S.55, A:G.56, A:G.56, A:E.98, A:G.112, A:Q.116 SFG.7: 17 residues within 4Å: Chain B: C.30, E.50, G.52, C.53, G.54, N.57, N.74, D.75, L.76, G.95, D.96, V.97, G.112, S.113, A.114, W.117, M.118 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.26, B:G.52, B:N.57, B:N.57, B:L.76, B:D.96, B:D.96, B:V.97, B:S.113 Water bridges: B:G.56, B:G.56, B:G.112, B:Q.116

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: V.25, Q.28, I.29, N.32, S.184, T.186, P.240, Y.242 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.25, A:N.32, A:T.186, A:Y.242 Water bridges: B:Q.10, B:K.14, B:K.14 GOL.8: 9 residues within 4Å: Chain A: K.14 Chain B: V.25, Q.28, I.29, N.32, S.184, T.186, P.240, Y.242 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.25, B:S.184, B:T.186, A:K.14 Water bridges: B:N.32

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

SO4.3: 2 residues within 4Å: Chain A: P.42, S.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.43, A:S.43 SO4.4: 6 residues within 4Å: Chain A: Q.116, W.117, F.143, N.147, L.159, Y.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.116, A:W.117, A:N.147 SO4.5: 1 residues within 4Å: Chain A: H.127 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.127 SO4.9: 6 residues within 4Å: Chain B: Q.116, W.117, F.143, N.147, L.159, Y.161 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.116, B:W.117, B:N.147 Water bridges: B:Y.161 SO4.10: 2 residues within 4Å: Chain B: K.146, Q.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.183 Salt bridges: B:K.146 SO4.11: 2 residues within 4Å: Chain A: K.14 Chain B: K.14 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:N.32, B:K.14, B:N.35 Salt bridges: A:K.14, B:K.14 Hydrogen bonds: B:N.32

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.6: 6 residues within 4Å: Chain A: E.185, Q.187, Y.189 Chain B: R.11, F.12, A.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, Z. et al., A bacterial methyltransferase that initiates biotin synthesis, an attractive anti-ESKAPE druggable pathway. Sci Adv (2024)

Release Date

2024-11-13

Peptides

Malonyl-[acyl-carrier protein] O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Malonyl-[acyl-carrier protein] O-methyltransferase

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