SMTL ID : 6o6e.1

Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-1-1-mer

Ligands

13 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 2 residues within 4Å: Chain A: D.23, K.61 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.61 FMT.2: 3 residues within 4Å: Chain A: E.227, S.228, F.231 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.67, A:E.227 FMT.3: 1 residues within 4Å: Chain A: Q.242 No protein-ligand interaction detected (PLIP) FMT.4: 3 residues within 4Å: Chain A: R.54, F.368, A.369 No protein-ligand interaction detected (PLIP) FMT.5: 2 residues within 4Å: Chain A: G.360, P.361 No protein-ligand interaction detected (PLIP) FMT.6: 4 residues within 4Å: Chain A: S.62, D.64, L.126, D.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.62, A:D.64 FMT.7: 4 residues within 4Å: Chain A: P.129, A.130, S.131, N.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 FMT.8: 5 residues within 4Å: Chain A: Q.373, P.376, Y.377, K.378 Ligands: FMT.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.373, A:K.378 FMT.9: 4 residues within 4Å: Chain A: P.371, A.372, Q.373 Ligands: FMT.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.373 FMT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.11: 2 residues within 4Å: Chain A: W.339, R.347 No protein-ligand interaction detected (PLIP) FMT.12: 5 residues within 4Å: Chain A: K.61, H.200, V.225, P.226, E.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.61 FMT.13: 2 residues within 4Å: Chain A: E.39, R.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.39, A:R.136, A:T.140

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 8 residues within 4Å: Chain A: L.365, G.366, Y.367, F.368, A.369, K.370, P.371, A.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.365, A:A.369

2 x MLA: MALONIC ACID(Non-covalent)

MLA.15: 2 residues within 4Å: Chain A: R.17, E.31 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.17 MLA.16: 10 residues within 4Å: Chain A: P.305, E.307, Y.367, Y.377, T.379, R.396, D.398, M.400, R.407, E.409 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.367, A:Y.367, A:Y.377 Salt bridges: A:R.396, A:R.396, A:R.407, A:R.407

1 x I5M: 5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine(Covalent)

I5M.17: 33 residues within 4Å: Chain A: H.200, F.205, D.206, L.207, F.231, Y.249, V.251, S.253, V.254, M.257, A.278, G.279, E.280, P.281, N.301, L.302, F.303, G.304, P.305, T.306, N.309, V.310, D.381, Y.393, R.396, M.400, R.404, G.405, N.406, R.407 Chain B: N.41, S.42, M.43 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.205, A:V.251, A:V.251, A:A.278, A:V.310 Hydrogen bonds: A:G.279, A:N.301, A:G.304, A:G.304, A:T.306, A:T.306, A:Y.393, A:R.396, A:R.404, A:G.405, A:N.406, A:R.407, B:S.42, B:S.42 Water bridges: A:N.301 Salt bridges: A:R.404 pi-Stacking: A:Y.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corpuz, J.C. et al., Dynamic visualization of type II peptidyl carrier protein recognition in pyoluteorin biosynthesis. Rsc Chem Biol (2020)

Release Date

2020-04-08

Peptides

L-proline--[L-prolyl-carrier protein] ligase: A
Peptidyl carrier protein PltL: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

L-proline--[L-prolyl-carrier protein] ligase

Peptidyl carrier protein PltL

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