SMTL ID : 7zcc.1 (1 other biounit)

yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: H.156, D.158, H.235 Ligands: OGA.2, GOL.3, GOL.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.156, A:D.158, A:H.235, H2O.3 MN.10: 6 residues within 4Å: Chain B: H.156, D.158, H.235 Ligands: OGA.11, GOL.12, GOL.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.156, B:D.158, B:H.235

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 16 residues within 4Å: Chain A: Y.145, G.152, F.153, H.156, D.158, N.162, I.164, K.171, W.173, L.229, H.235, T.237, N.247 Ligands: MN.1, GOL.3, GOL.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.237, A:T.237, A:N.247 Water bridges: A:K.171, A:K.171, A:K.171 Salt bridges: A:K.171, A:H.235 OGA.11: 16 residues within 4Å: Chain B: Y.145, G.152, F.153, H.156, D.158, N.162, I.164, K.171, W.173, L.229, H.235, T.237, N.247 Ligands: MN.10, GOL.12, GOL.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.145, B:N.162, B:T.237, B:N.247 Water bridges: B:K.171 Salt bridges: B:K.171, B:H.235

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: R.91, E.110, Y.145, F.153, H.156, D.158, H.187 Ligands: MN.1, OGA.2, GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.91, A:E.110, A:D.158, A:D.158 GOL.4: 8 residues within 4Å: Chain A: A.176, K.177, N.178, E.179, P.209, D.215, A.216, W.234 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.177, A:E.179 Water bridges: A:E.179, A:D.215, A:D.215 GOL.5: 9 residues within 4Å: Chain A: S.139, A.159, Y.160, M.185, G.251, Q.252, P.253, F.322, D.323 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.139, A:A.159, A:M.185, A:Q.252, A:D.323, A:D.323 GOL.6: 11 residues within 4Å: Chain A: K.141, I.143, Y.145, D.158, Y.160, N.162, N.247, T.249 Ligands: MN.1, OGA.2, GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.145, A:N.162, A:N.162, A:N.247 Water bridges: A:D.158 GOL.7: 7 residues within 4Å: Chain A: I.54, P.55, G.56, F.57, E.58, K.59, Q.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.56, A:E.58, A:Q.120 GOL.12: 10 residues within 4Å: Chain B: R.91, E.110, Y.145, F.153, H.156, D.158, H.187 Ligands: MN.10, OGA.11, GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.91, B:Y.145 Water bridges: B:R.91 GOL.13: 11 residues within 4Å: Chain B: K.141, I.143, Y.145, D.158, Y.160, N.162, N.247, T.249 Ligands: MN.10, OGA.11, GOL.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.145, B:D.158, B:N.162, B:N.162, B:N.247, B:T.249 Water bridges: B:D.158

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

SO4.8: 3 residues within 4Å: Chain A: T.28, S.30, E.31 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.28, A:S.30, A:E.31, A:E.31 Water bridges: A:T.28, A:S.30 SO4.9: 6 residues within 4Å: Chain A: K.154, A.155, K.174, D.212, L.213, S.236 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.155, A:D.212, A:S.236, A:S.236 Water bridges: A:K.174 Salt bridges: A:K.154, A:K.174 SO4.14: 4 residues within 4Å: Chain B: P.26, V.27, T.28, E.31 No protein-ligand interaction detected (PLIP) SO4.15: 3 residues within 4Å: Chain B: L.283, H.284, S.287 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.284, B:S.287 Salt bridges: B:H.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG). To Be Published

Release Date

2023-04-05

Peptides

Uncharacterized protein YxbC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein YxbC

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