SMTL ID : 6ulx.1

Adenylation domain of a keto acid-selecting NRPS module bound to keto acyl adenylate space group P43212

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

1 x QA7: 5'-O-{(S)-hydroxy[(4-methyl-2-oxopentanoyl)oxy]phosphoryl}adenosine(Non-covalent)

QA7.1: 23 residues within 4Å: Chain A: H.223, I.224, G.225, M.229, W.269, G.301, A.302, E.303, A.304, V.305, A.330, F.331, G.332, M.333, S.334, E.335, S.338, A.339, L.383, T.440, D.442, L.453, R.456 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.302, A:A.330, A:G.332, A:S.334, A:S.334, A:D.442 Water bridges: A:V.305, A:V.305 Salt bridges: A:H.223, A:H.223 pi-Stacking: A:F.331

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

SO4.2: 6 residues within 4Å: Chain A: Y.34, V.36, S.77, N.78, H.79, R.245 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.61, K.66, A.67, H.166 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: H.115, H.116, K.119, M.185 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: K.323, G.324, R.348 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: R.348, G.349 Ligand excluded by PLIP SO4.7: 9 residues within 4Å: Chain A: S.76, N.78, M.81, P.220, L.221, R.243, A.244, R.245, T.246 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: A.251, Q.252, R.255 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: N.396, H.397, R.409, H.469 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: E.303, A.304, R.456, K.561, Q.565 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: S.343, F.344, A.345, G.384, K.385, R.450 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: R.55, E.160, R.161 Ligand excluded by PLIP SO4.13: 7 residues within 4Å: Chain A: N.207, F.209, D.213, K.267, T.296, C.297, R.328 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: E.365, Q.366, H.406 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain A: A.276, N.279, T.309, R.312, A.558, Q.559, T.562 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain A: T.29, G.31, L.32, T.33, T.43, Q.44, S.45, E.240 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain A: H.115, W.118, K.119, H.123, T.145 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain A: Q.48 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alonzo, D.A. et al., Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis. Nat.Chem.Biol. (2020)

Release Date

2020-02-19

Peptides

Amino acid adenylation domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Amino acid adenylation domain-containing protein

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