SMTL ID : 2pr1.2 (1 other biounit)

Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 4 residues within 4Å: Chain A: E.8, Y.54, G.56, D.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.57 GLC-FRU.2: 9 residues within 4Å: Chain B: E.8, L.11, Y.54, D.57 Chain D: K.111, P.151, D.152, M.153 Ligands: SO4.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:E.8, D:K.111, D:D.152, D:K.111, D:K.111 GLC-FRU.9: 4 residues within 4Å: Chain C: E.8, Y.54, G.56, D.57 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.57 GLC-FRU.10: 9 residues within 4Å: Chain B: K.111, P.151, D.152, M.153 Chain D: E.8, L.11, Y.54, D.57 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.111, B:D.152, B:K.111, B:K.111

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

SO4.3: 5 residues within 4Å: Chain A: Y.66, Q.67, V.68, N.69 Chain B: A.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.69, A:N.69 SO4.7: 4 residues within 4Å: Chain B: K.108, N.130, W.149 Ligands: GLC-FRU.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.149 Salt bridges: B:K.108 SO4.11: 5 residues within 4Å: Chain C: Y.66, Q.67, V.68, N.69 Chain D: A.139 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.66, C:N.69, C:N.69 SO4.15: 4 residues within 4Å: Chain D: K.108, N.130, W.149 Ligands: GLC-FRU.2 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.149 Salt bridges: D:K.108

4 x COA: COENZYME A(Non-covalent)

COA.4: 16 residues within 4Å: Chain A: L.88, E.89, V.90, Y.94, Q.95, N.96, R.97, G.98, Y.99, G.100, R.101, K.121, S.122, E.124, F.125, K.128 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.88 Hydrogen bonds: A:V.90, A:Q.95, A:N.96, A:R.97, A:G.98, A:G.98, A:Y.99, A:G.100, A:R.101, A:S.122 Salt bridges: A:R.101, A:K.128 COA.8: 14 residues within 4Å: Chain B: E.89, V.90, Q.95, N.96, R.97, G.98, Y.99, G.100, R.101, R.119, S.122, E.124, F.125, K.128 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.125 Hydrogen bonds: B:V.90, B:Q.95, B:N.96, B:G.98, B:G.98, B:G.100, B:R.101, B:R.119 Salt bridges: B:R.101, B:K.128 COA.12: 16 residues within 4Å: Chain C: L.88, E.89, V.90, Y.94, Q.95, N.96, R.97, G.98, Y.99, G.100, R.101, K.121, S.122, E.124, F.125, K.128 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.88 Hydrogen bonds: C:V.90, C:Q.95, C:N.96, C:R.97, C:G.98, C:G.98, C:Y.99, C:G.100, C:R.101, C:S.122 Salt bridges: C:R.101, C:K.128 COA.16: 14 residues within 4Å: Chain D: E.89, V.90, Q.95, N.96, R.97, G.98, Y.99, G.100, R.101, R.119, S.122, E.124, F.125, K.128 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.125 Hydrogen bonds: D:V.90, D:Q.95, D:N.96, D:G.98, D:G.98, D:G.100, D:R.101, D:R.119 Salt bridges: D:R.101, D:K.128

4 x CO: COBALT (II) ION(Non-covalent)

CO.5: 2 residues within 4Å: Chain B: W.149, H.150 No protein-ligand interaction detected (PLIP) CO.6: 3 residues within 4Å: Chain D: T.5, E.105, F.106 No protein-ligand interaction detected (PLIP) CO.13: 2 residues within 4Å: Chain D: W.149, H.150 No protein-ligand interaction detected (PLIP) CO.14: 3 residues within 4Å: Chain B: T.5, E.105, F.106 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A. To be Published

Release Date

2007-05-15

Peptides

Uncharacterized N-acetyltransferase ylbP: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Uncharacterized N-acetyltransferase ylbP

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