SMTL ID : 6uly.1

Adenylation domain of a keto acid-selecting NRPS module bound to keto acyl adenylate space group P212121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

QA7.1: 22 residues within 4Å: Chain A: H.223, I.224, G.225, M.229, W.269, I.299, G.301, A.302, E.303, A.304, V.305, A.330, F.331, G.332, M.333, S.334, S.338, A.339, L.383, D.442, L.453, R.456 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.339 Hydrogen bonds: A:A.302, A:A.330, A:G.332, A:S.334, A:D.442 Salt bridges: A:H.223, A:H.223 pi-Stacking: A:F.331 QA7.16: 23 residues within 4Å: Chain B: S.180, 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, S.338, A.339, L.383, T.440, D.442, L.453, R.456 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.339 Hydrogen bonds: B:S.180, B:A.302, B:A.330, B:G.332, B:S.334, B:D.442 Salt bridges: B:H.223, B:H.223 pi-Stacking: B:F.331

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

SO4.2: 7 residues within 4Å: Chain A: Y.34, I.35, V.36, S.77, N.78, H.79, R.245 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: K.323, G.324, R.348 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: Q.48, R.55 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: R.55, E.160, R.161 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: R.161, T.163 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: K.66, A.67, H.166 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: H.115, W.118, K.119, H.123, W.143, T.145 Chain B: A.434 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain A: H.399, R.409, Q.433, H.439, E.457 Chain B: K.112 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: R.348, G.349 Ligand excluded by PLIP SO4.11: 7 residues within 4Å: Chain A: H.115, H.116, K.119, M.185 Chain B: Q.429, E.430, Q.433 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: D.248, A.251, Q.252, R.255 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: N.37, S.38, R.255 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: E.303, A.304, K.561, Q.565 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: K.323, G.324, R.348 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain B: Y.34, V.36, S.77, N.78, H.79, R.245 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain A: Q.429, E.430, Q.433 Chain B: H.115, H.116, K.119 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: D.248, A.251, Q.252, R.255 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: H.315, R.348, G.349 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: R.61, K.66, A.67, H.166 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: N.37, S.38, R.255 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain A: K.112 Chain B: H.399, R.409, Q.433, H.439, E.457 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 8 residues within 4Å: Chain A: Q.433, A.434 Chain B: H.115, W.118, K.119, H.123, T.145, Q.147 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.115, B:K.119, B:H.123, A:A.434

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amino acid adenylation domain-containing protein

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