SMTL ID : 4qvt.5 (4 other biounits)

Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-octamer

Ligands

8 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 20 residues within 4Å: Chain A: C.21, L.23, A.69, Y.70, Y.71, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, V.114, M.117, Y.118, R.120 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.72, A:L.72, A:V.74, A:A.84 Hydrogen bonds: A:V.74, A:R.79, A:G.80, A:R.81, A:G.82, A:G.82, A:I.83, A:A.84, A:N.85, A:Y.118, A:R.120 Water bridges: A:F.78 Salt bridges: A:R.120 ACO.4: 19 residues within 4Å: Chain B: C.21, L.23, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, V.114, M.117, Y.118, R.120 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.72, B:L.72 Hydrogen bonds: B:V.74, B:G.80, B:G.82, B:G.82, B:I.83, B:A.84, B:N.85, B:N.85, B:R.120 Water bridges: B:R.81, B:R.81 Salt bridges: B:R.120 ACO.6: 18 residues within 4Å: Chain C: C.21, L.23, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, M.117, Y.118, R.120 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.72 Hydrogen bonds: C:V.74, C:R.79, C:G.80, C:R.81, C:G.82, C:I.83, C:A.84, C:N.85, C:N.85, C:Y.118 Water bridges: C:F.78, C:N.85, C:N.85 Salt bridges: C:R.120 ACO.8: 17 residues within 4Å: Chain D: C.21, L.23, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, M.117, Y.118 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.72, D:L.72, D:A.84 Hydrogen bonds: D:V.74, D:G.80, D:R.81, D:G.82, D:G.82, D:I.83, D:A.84, D:N.85, D:N.85, D:Y.118 Water bridges: D:F.78, D:R.79, D:R.120 ACO.10: 19 residues within 4Å: Chain E: C.21, L.23, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, V.114, M.117, Y.118, R.120 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:L.72, E:L.72, E:A.84 Hydrogen bonds: E:V.74, E:R.79, E:G.80, E:G.82, E:G.82, E:I.83, E:A.84, E:N.85, E:N.85, E:R.120 Water bridges: E:F.78, E:R.81 Salt bridges: E:R.120 ACO.14: 17 residues within 4Å: Chain F: C.21, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, M.117, Y.118, R.120 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:L.72, F:L.72, F:V.74, F:A.84 Hydrogen bonds: F:V.74, F:G.80, F:R.81, F:G.82, F:G.82, F:I.83, F:A.84, F:N.85, F:N.85, F:Y.118, F:R.120 Salt bridges: F:R.120 ACO.15: 18 residues within 4Å: Chain G: C.21, L.23, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, M.117, Y.118, R.120 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:L.72 Hydrogen bonds: G:V.74, G:R.79, G:G.80, G:R.81, G:G.82, G:I.83, G:A.84, G:N.85, G:N.85, G:N.85, G:R.120 Water bridges: G:F.78, G:R.79 Salt bridges: G:R.120 ACO.18: 18 residues within 4Å: Chain H: C.21, L.23, A.69, Y.70, L.72, G.73, V.74, R.79, G.80, R.81, G.82, I.83, A.84, N.85, M.113, M.117, Y.118, R.120 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:L.72, H:V.74, H:A.84 Hydrogen bonds: H:V.74, H:R.79, H:G.80, H:R.81, H:G.82, H:G.82, H:I.83, H:A.84, H:N.85, H:N.85, H:R.120 Water bridges: H:N.111 Salt bridges: H:R.120

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

SO4.2: 2 residues within 4Å: Chain A: R.7, Q.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.8, A:Q.8 Water bridges: A:E.9 SO4.3: 4 residues within 4Å: Chain A: W.27, N.28 Chain B: R.66, K.102 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Water bridges: B:R.66, B:K.102, A:R.134 Salt bridges: B:R.66, B:K.102 Hydrogen bonds: A:N.28, A:N.28 SO4.5: 4 residues within 4Å: Chain A: R.66, K.102 Chain B: W.27, N.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.66, A:K.102 Hydrogen bonds: B:N.28 SO4.7: 4 residues within 4Å: Chain C: R.66, K.102 Chain D: W.27, N.28 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.28, C:Q.104 Water bridges: D:R.134 Salt bridges: C:R.66, C:K.102 SO4.9: 4 residues within 4Å: Chain C: W.27, N.28 Chain D: R.66, K.102 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.28 Salt bridges: D:R.66, D:K.102 SO4.11: 4 residues within 4Å: Chain E: R.66, K.102 Chain F: W.27, N.28 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:W.27, F:N.28 Salt bridges: E:R.66, E:K.102 SO4.12: 4 residues within 4Å: Chain E: W.27, N.28 Chain F: R.66, K.102 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:N.28, F:Q.104 Salt bridges: F:R.66, F:K.102 SO4.13: 2 residues within 4Å: Chain E: R.7, Q.8 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.8, E:Q.8 Salt bridges: E:R.7 SO4.16: 4 residues within 4Å: Chain G: W.27, N.28 Chain H: R.66, K.102 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G Salt bridges: H:R.66, H:K.102 Hydrogen bonds: G:W.27, G:N.28 SO4.17: 4 residues within 4Å: Chain G: R.66, K.102 Chain H: W.27, N.28 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Salt bridges: G:R.66, G:K.102 Hydrogen bonds: H:N.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli. To be Published

Release Date

2014-07-30

Peptides

Acetyltransferase YpeA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Acetyltransferase YpeA

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