SMTL ID : 6ia5.1

Crystal Structure Analysis of Bacillus subtilis 168 XepA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-pentamer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: G.17, A.18 Chain E: A.16 Ligands: GOL.16, GOL.22 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:A.16, A:A.18 GOL.2: 6 residues within 4Å: Chain A: R.23, N.27, D.28 Chain B: A.40, E.41 Chain D: K.20 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.23, A:N.27, D:K.20 Water bridges: A:N.27, D:E.7 GOL.8: 6 residues within 4Å: Chain B: A.16 Chain C: F.8, A.16, G.17, A.18 Ligands: ACT.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.18 GOL.9: 5 residues within 4Å: Chain B: E.85, W.93, T.95, R.120, R.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.95 Water bridges: B:W.93, B:T.95, B:T.95 GOL.10: 6 residues within 4Å: Chain B: S.87, D.88, N.89, V.92, T.94, K.116 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.88, B:N.89, B:K.116, B:K.116 GOL.16: 6 residues within 4Å: Chain C: A.16, G.17 Chain E: F.8, A.16, A.18 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.18 GOL.17: 5 residues within 4Å: Chain A: E.41 Chain C: R.23, N.27, D.28 Chain E: K.20 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: C:R.23, C:D.28, C:D.28, E:K.20 Water bridges: C:N.27, C:N.27, A:I.42 GOL.18: 6 residues within 4Å: Chain C: S.87, D.88, N.89, V.92, T.94, K.116 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.88, C:N.89, C:N.89, C:K.116, C:K.116 GOL.19: 3 residues within 4Å: Chain C: T.94, T.95, T.96 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.94, C:T.94 GOL.22: 8 residues within 4Å: Chain A: K.15, A.16, G.17 Chain D: F.8, A.16, A.18 Ligands: GOL.1, ACT.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.18 GOL.29: 8 residues within 4Å: Chain C: K.71, W.73, A.108 Chain E: R.61, S.68, L.114, S.115 Ligands: ACT.21 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:K.71, C:K.71, E:R.61, E:R.61, E:S.115 Water bridges: C:K.71

22 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: N.35 Chain E: S.34, N.35 Ligands: ACT.26, ACT.32 Ligand excluded by PLIP ACT.4: 5 residues within 4Å: Chain A: S.87, D.88, N.89, V.92, K.116 Ligand excluded by PLIP ACT.5: 4 residues within 4Å: Chain A: A.50, N.127, L.128, Q.129 Ligand excluded by PLIP ACT.6: 4 residues within 4Å: Chain A: Y.75, E.132 Chain D: N.89, Y.118 Ligand excluded by PLIP ACT.7: 4 residues within 4Å: Chain A: H.200, A.250, D.252 Ligands: ACT.28 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain B: R.23, N.27, D.28 Chain C: K.20 Chain E: E.41 Ligand excluded by PLIP ACT.12: 7 residues within 4Å: Chain B: N.35 Chain C: M.144 Chain D: V.33, S.34, N.35 Ligands: ACT.20, ACT.26 Ligand excluded by PLIP ACT.13: 6 residues within 4Å: Chain A: N.149 Chain B: K.71, T.109, D.110, W.111 Chain E: R.147 Ligand excluded by PLIP ACT.14: 2 residues within 4Å: Chain B: E.132 Chain C: N.89 Ligand excluded by PLIP ACT.15: 3 residues within 4Å: Chain B: A.18 Ligands: GOL.8, GOL.22 Ligand excluded by PLIP ACT.20: 7 residues within 4Å: Chain B: V.33, S.34, N.35 Chain C: N.35 Chain E: M.144 Ligands: ACT.12, ACT.32 Ligand excluded by PLIP ACT.21: 7 residues within 4Å: Chain A: R.147 Chain C: K.71, D.110, W.111 Chain D: N.149, K.151 Ligands: GOL.29 Ligand excluded by PLIP ACT.23: 5 residues within 4Å: Chain C: R.147 Chain D: K.71, D.110, W.111 Chain E: K.151 Ligand excluded by PLIP ACT.24: 5 residues within 4Å: Chain B: N.149 Chain D: R.147 Chain E: K.71, D.110, W.111 Ligand excluded by PLIP ACT.25: 2 residues within 4Å: Chain D: E.213, L.243 Ligand excluded by PLIP ACT.26: 8 residues within 4Å: Chain A: V.33, S.34, N.35 Chain B: M.144 Chain D: N.35 Chain E: V.33 Ligands: ACT.3, ACT.12 Ligand excluded by PLIP ACT.27: 2 residues within 4Å: Chain D: K.215, S.241 Ligand excluded by PLIP ACT.28: 6 residues within 4Å: Chain A: H.200, A.250 Chain D: D.252, K.254, F.256 Ligands: ACT.7 Ligand excluded by PLIP ACT.30: 2 residues within 4Å: Chain E: K.215, S.241 Ligand excluded by PLIP ACT.31: 1 residues within 4Å: Chain E: E.213 Ligand excluded by PLIP ACT.32: 9 residues within 4Å: Chain A: M.144 Chain B: V.33 Chain C: V.33, S.34, N.35 Chain E: N.35, M.144 Ligands: ACT.3, ACT.20 Ligand excluded by PLIP ACT.33: 5 residues within 4Å: Chain E: S.87, D.88, N.89, V.92, K.116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freitag-Pohl, S. et al., Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-11-20

Peptides

Phage-like element PBSX protein XepA: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
C

D
B

E
E

Phage-like element PBSX protein XepA

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