SMTL ID : 4qus.2 (1 other biounit)

1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-octamer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: R.66, K.102 Chain B: W.27, N.28 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:K.102, A:K.102, A:K.102, A:Q.104, B:W.27 Salt bridges: A:R.66, A:K.102 Hydrogen bonds: B:N.28 PO4.2: 4 residues within 4Å: Chain A: W.27, N.28 Chain B: R.66, K.102 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.28 Water bridges: B:R.66, B:K.102 Salt bridges: B:R.66, B:K.102 PO4.6: 4 residues within 4Å: Chain C: R.66, K.102 Chain D: W.27, N.28 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Water bridges: C:K.102, C:K.102, C:K.102, C:Q.104, D:W.27 Salt bridges: C:R.66, C:K.102 Hydrogen bonds: D:N.28 PO4.7: 4 residues within 4Å: Chain C: W.27, N.28 Chain D: R.66, K.102 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Water bridges: D:R.66, D:K.102 Salt bridges: D:R.66, D:K.102 Hydrogen bonds: C:N.28 PO4.11: 4 residues within 4Å: Chain E: R.66, K.102 Chain F: W.27, N.28 8 PLIP interactions: 2 interactions with chain F, 6 interactions with chain E Hydrogen bonds: F:N.28 Water bridges: F:W.27, E:K.102, E:K.102, E:K.102, E:Q.104 Salt bridges: E:R.66, E:K.102 PO4.12: 4 residues within 4Å: Chain E: W.27, N.28 Chain F: R.66, K.102 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Water bridges: F:R.66, F:K.102 Salt bridges: F:R.66, F:K.102 Hydrogen bonds: E:N.28 PO4.16: 4 residues within 4Å: Chain G: R.66, K.102 Chain H: W.27, N.28 8 PLIP interactions: 6 interactions with chain G, 2 interactions with chain H Water bridges: G:K.102, G:K.102, G:K.102, G:Q.104, H:W.27 Salt bridges: G:R.66, G:K.102 Hydrogen bonds: H:N.28 PO4.17: 4 residues within 4Å: Chain G: W.27, N.28 Chain H: R.66, K.102 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Water bridges: H:R.66, H:K.102 Salt bridges: H:R.66, H:K.102 Hydrogen bonds: G:N.28

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

EDO.3: 4 residues within 4Å: Chain A: H.40, D.41 Chain B: H.40, D.41 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.41, A:D.41, B:D.41 EDO.4: 2 residues within 4Å: Chain B: Y.70, Y.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.71 Water bridges: B:N.28, B:L.72, B:N.106, B:N.106 EDO.5: 4 residues within 4Å: Chain B: R.79, G.80, R.81, G.82 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.80, B:G.82 Water bridges: B:G.82, B:I.83, B:I.83, B:A.84 EDO.8: 4 residues within 4Å: Chain C: H.40, D.41 Chain D: H.40, D.41 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.41, C:D.41, D:D.41 EDO.9: 2 residues within 4Å: Chain D: Y.70, Y.71 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.71 Water bridges: D:N.28, D:L.72, D:N.106, D:N.106 EDO.10: 4 residues within 4Å: Chain D: R.79, G.80, R.81, G.82 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.80, D:G.82 Water bridges: D:G.82, D:I.83, D:I.83, D:A.84 EDO.13: 4 residues within 4Å: Chain E: H.40, D.41 Chain F: H.40, D.41 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:D.41, E:D.41, E:D.41 EDO.14: 2 residues within 4Å: Chain F: Y.70, Y.71 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.71 Water bridges: F:N.28, F:L.72, F:N.106, F:N.106 EDO.15: 4 residues within 4Å: Chain F: R.79, G.80, R.81, G.82 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.80, F:G.82 Water bridges: F:G.82, F:I.83, F:I.83, F:A.84 EDO.18: 4 residues within 4Å: Chain G: H.40, D.41 Chain H: H.40, D.41 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:D.41, G:D.41, G:D.41 EDO.19: 2 residues within 4Å: Chain H: Y.70, Y.71 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Y.71 Water bridges: H:N.28, H:L.72, H:N.106, H:N.106 EDO.20: 4 residues within 4Å: Chain H: R.79, G.80, R.81, G.82 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:G.80, H:G.82 Water bridges: H:G.82, H:I.83, H:I.83, H:A.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., 1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655. To be Published

Release Date

2014-07-23

Peptides

Acetyltransferase YpeA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Acetyltransferase YpeA

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