SMTL ID : 4rvn.1 (1 other biounit)

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.252, H.259, C.314, C.316 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.252, A:H.259, A:C.314, A:C.316 ZN.15: 4 residues within 4Å: Chain B: C.252, H.259, C.314, C.316 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.252, B:H.259, B:C.314, B:C.316

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain A: G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, I.335, N.340 Ligands: K.4, UNL.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.143, A:T.143, A:A.215, A:S.237, A:G.239, A:T.241, A:T.241, A:D.305, A:R.329, A:N.340 Water bridges: A:N.236, A:N.236, A:T.241, A:N.340 AMP.16: 16 residues within 4Å: Chain B: S.95, G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, K.425 Ligands: UNL.17 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.95, B:S.95, B:A.215, B:S.237, B:G.239, B:T.241, B:D.305, B:R.329, B:K.425 Water bridges: B:S.94, B:N.236, B:I.326, B:R.329, B:R.329 Salt bridges: B:K.425

1 x COA: COENZYME A(Non-covalent)

COA.3: 12 residues within 4Å: Chain A: S.136, A.164, G.165, N.166, S.167, I.185, Y.188, R.191, K.337, Q.370, V.407, T.408 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.165, A:N.166, A:S.167, A:S.167, A:S.167, A:K.337, A:Q.370, A:T.408, A:T.408, A:T.408 Water bridges: A:K.168, A:I.185 Salt bridges: A:R.191, A:K.337, A:K.337 pi-Stacking: A:Y.188

3 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: A.215, G.338, N.340 Ligands: AMP.2, UNL.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.215 K.5: 7 residues within 4Å: Chain A: K.129, G.156, C.157, L.158 Chain B: M.84, K.85, G.88 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:K.129, A:G.156, B:K.85, B:G.88 K.6: 8 residues within 4Å: Chain A: M.84, K.85, R.86, G.88 Chain B: K.129, G.156, C.157, L.158 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:K.85, A:G.88, B:K.129, B:G.156, H2O.3

2 x UNL: UNKNOWN LIGAND

UNL.7: 12 residues within 4Å: Chain A: S.137, F.142, T.143, G.144, F.148, A.215, G.239, T.241, P.246, G.338 Ligands: AMP.2, K.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.137, A:S.137, A:S.137, A:T.143, A:G.144, A:A.215, A:A.215, A:G.239 Water bridges: A:T.241, A:G.338, A:N.340 UNL.17: 13 residues within 4Å: Chain B: S.93, S.137, F.142, T.143, G.144, A.215, S.237, G.239, T.241, G.245, P.246, K.425 Ligands: AMP.16 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.95, B:S.95, B:S.137, B:S.137, B:T.143, B:T.143, B:T.143, B:G.144, B:A.215, B:G.239, B:K.425

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

SO4.8: 3 residues within 4Å: Chain A: G.48, S.53, K.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.52 Salt bridges: A:K.62 SO4.9: 2 residues within 4Å: Chain A: R.394, R.395 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.394 Salt bridges: A:R.394, A:R.395 SO4.18: 4 residues within 4Å: Chain B: N.166, S.167, Y.188, R.191 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.166, B:S.167, B:S.167, B:Y.188 Water bridges: B:N.166, B:K.168 Salt bridges: B:R.191

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 6 residues within 4Å: Chain A: I.31, N.32, A.35, F.44, I.49, T.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:I.49 EDO.11: 1 residues within 4Å: Chain A: K.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.46 Water bridges: A:K.46 EDO.12: 7 residues within 4Å: Chain A: M.71, N.74, Y.75, P.76, T.102, V.103, M.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.103 EDO.13: 5 residues within 4Å: Chain A: Q.23, L.57, E.262, L.266, V.267 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.23, A:E.262, A:V.267, A:V.267 Water bridges: A:Q.23 EDO.14: 2 residues within 4Å: Chain A: I.33, E.294 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.87 EDO.19: 5 residues within 4Å: Chain B: N.47, R.61, K.62, I.63, P.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.47, B:R.61 Water bridges: B:F.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution. To be published

Release Date

2015-01-21

Peptides

Phenylacetate-coenzyme A ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phenylacetate-coenzyme A ligase

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