SMTL ID : 4pf1.1

Crystal structure of aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: W.350, N.354, L.376, W.385, R.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.387 PGE.7: 3 residues within 4Å: Chain B: W.350 Chain C: E.344, W.350 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.344 PGE.14: 3 residues within 4Å: Chain A: W.350, W.385 Chain D: W.350 No protein-ligand interaction detected (PLIP) PGE.19: 6 residues within 4Å: Chain D: W.350, N.354, V.355, L.376, W.385, R.387 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.387

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Q.330, R.333, D.334, S.337, L.338, G.339, E.455 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.330, A:R.333, A:R.333, A:D.334, A:G.339, A:E.455 Water bridges: A:D.334 GOL.3: 9 residues within 4Å: Chain A: Y.165, M.187, V.188, D.189, G.190, W.196, W.269, Q.272, M.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.190, A:W.196, A:Q.272 GOL.4: 6 residues within 4Å: Chain A: L.341, Q.342, F.343, G.381, N.383, W.511 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.342, A:G.381, A:N.383 GOL.5: 8 residues within 4Å: Chain A: Y.69, S.161, M.187, D.195, W.196, A.206, Y.210, E.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.206, A:E.297 Water bridges: A:S.161, A:Y.162, A:E.297 GOL.6: 4 residues within 4Å: Chain A: Q.423, A.424, F.425, R.612 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.423, A:F.425, A:F.425, A:R.612, A:R.612 GOL.8: 6 residues within 4Å: Chain B: L.341, Q.342, T.380, G.381, N.383, W.511 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.342, B:G.381, B:N.383 Water bridges: B:P.340 GOL.9: 9 residues within 4Å: Chain B: N.119, Y.165, M.187, V.188, D.189, G.190, W.196, W.269, Q.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.187, B:G.190, B:W.196 Water bridges: B:D.189 GOL.10: 8 residues within 4Å: Chain B: Y.69, S.161, M.187, D.195, W.196, A.206, Y.210, E.297 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.69, B:S.161, B:A.206, B:E.297 Water bridges: B:Y.162, B:E.297 GOL.11: 8 residues within 4Å: Chain C: N.119, M.187, V.188, D.189, G.190, W.196, W.269, Q.272 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.190, C:W.269 GOL.12: 7 residues within 4Å: Chain C: L.341, Q.342, F.343, T.380, G.381, N.383, W.511 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.342, C:Q.342, C:G.381, C:N.383 Water bridges: C:P.340 GOL.13: 3 residues within 4Å: Chain C: H.70, E.72, R.73 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.72, C:E.72, C:R.73, C:R.73 Water bridges: C:H.70 GOL.15: 7 residues within 4Å: Chain D: L.341, Q.342, F.343, T.380, G.381, N.383, W.511 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.342, D:G.381, D:N.383 GOL.16: 4 residues within 4Å: Chain D: N.327, G.329, Q.330, R.333 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.327, D:N.327, D:G.329, D:R.333 Water bridges: D:Q.296, D:G.454 GOL.17: 8 residues within 4Å: Chain D: Y.69, S.161, M.187, D.195, W.196, A.206, Y.210, E.297 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.161, D:A.206, D:E.297 Water bridges: D:D.195, D:Y.210 GOL.18: 4 residues within 4Å: Chain B: K.223, W.224, Y.447 Chain D: N.79 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalska, K. et al., New aminopeptidase from "microbial dark matter" archaeon. FASEB J. (2015)

Release Date

2014-06-11

Peptides

Peptidase S15/CocE/NonD: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Peptidase S15/CocE/NonD