SMTL ID : 6oz1.1

Crystal structure of the adenylation (A) domain of the carboxylate reductase (CAR) GR01_22995 from Mycobacterium chelonae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: S.329, D.330, T.612, V.613, E.614, R.622 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.613, A:E.614 Water bridges: A:D.330, A:R.622 Salt bridges: A:R.622 SO4.2: 1 residues within 4Å: Chain A: R.544 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.544, A:R.544, A:R.544 Salt bridges: A:R.544 SO4.3: 5 residues within 4Å: Chain A: G.265, S.266, K.271, R.515, K.517 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.266, A:R.515 Water bridges: A:T.267 Salt bridges: A:K.271, A:K.517 SO4.4: 3 residues within 4Å: Chain A: F.335, E.336, R.359 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.336 Water bridges: A:F.335, A:F.335, A:R.359 Salt bridges: A:R.359 SO4.5: 3 residues within 4Å: Chain A: S.251, E.252, D.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.252, A:D.253 SO4.6: 2 residues within 4Å: Chain A: Y.118, R.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.118 Salt bridges: A:R.123 SO4.7: 3 residues within 4Å: Chain A: D.71, S.102, R.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.102 Water bridges: A:S.102 Salt bridges: A:R.104 SO4.8: 3 residues within 4Å: Chain A: E.379, S.414, Q.417 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.417 Water bridges: A:E.379, A:S.414, A:S.414 Salt bridges: A:K.382

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain A: S.160, K.628 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: S.373, N.374 Ligand excluded by PLIP

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.11: 18 residues within 4Å: Chain A: T.263, H.306, G.400, S.401, A.402, P.403, D.422, G.423, Y.424, G.425, S.426, T.427, E.428, D.500, Y.512, R.515, K.623 Ligands: SIN.12 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.263, A:T.263, A:S.401, A:G.423, A:G.425, A:T.427, A:T.427, A:T.427, A:D.500, A:R.515, A:K.623 Water bridges: A:Y.424, A:S.426, A:S.426, A:Y.496, A:Y.496, A:T.498 Salt bridges: A:H.306, A:K.623 pi-Stacking: A:Y.424, A:Y.424

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.12: 10 residues within 4Å: Chain A: W.288, H.306, L.307, A.308, L.311, L.347, G.400, S.401, G.423 Ligands: AMP.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.308, A:L.311 Salt bridges: A:H.306

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain A: P.403, Y.512, R.515, N.518, S.531, K.623, L.624, R.626 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.512, A:S.531, A:R.626, A:R.626 Water bridges: A:L.624, A:R.626 GOL.14: 3 residues within 4Å: Chain A: P.406, K.511, K.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.511 GOL.15: 4 residues within 4Å: Chain A: E.413, Q.417, V.418, A.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.413 GOL.16: 2 residues within 4Å: Chain A: Y.556, R.602 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorchuk, T.P. et al., One-Pot Biocatalytic Transformation of Adipic Acid to 6-Aminocaproic Acid and 1,6-Hexamethylenediamine Using Carboxylic Acid Reductases and Transaminases. J.Am.Chem.Soc. (2020)

Release Date

2020-04-22

Peptides

Oxidoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oxidoreductase