SMTL ID : 2glf.1

Crystal structure of Aminipeptidase (M18 family) from Thermotoga Maritima

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-12-mer

Ligands

24 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: H.92, D.249, E.278, E.279, D.326 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:D.249, A:D.326, A:D.326, H2O.3 MN.2: 6 residues within 4Å: Chain A: D.249, E.278, E.279, M.424, H.425 Ligands: MN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.249, A:E.279, A:E.279, A:H.425 MN.3: 5 residues within 4Å: Chain B: D.249, E.279, M.424, H.425 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.249, B:E.279, B:E.279, B:H.425, H2O.8 MN.4: 5 residues within 4Å: Chain B: H.92, D.249, E.278, D.326 Ligands: MN.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.92, B:D.249, B:D.326, B:D.326, H2O.8 MN.5: 5 residues within 4Å: Chain C: H.92, D.249, E.278, D.326 Ligands: MN.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.92, C:D.249, C:D.326, C:D.326 MN.6: 6 residues within 4Å: Chain C: D.249, E.278, E.279, M.424, H.425 Ligands: MN.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.249, C:E.279, C:E.279, C:H.425 MN.7: 5 residues within 4Å: Chain D: H.92, D.249, E.278, D.326 Ligands: MN.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.92, D:D.249, D:D.326, D:D.326, H2O.17 MN.8: 6 residues within 4Å: Chain D: D.249, E.278, E.279, M.424, H.425 Ligands: MN.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.249, D:E.279, D:E.279, D:H.425, H2O.18 MN.9: 6 residues within 4Å: Chain E: H.92, D.249, E.278, E.279, D.326 Ligands: MN.10 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.92, E:D.249, E:D.326, E:D.326, H2O.22 MN.10: 6 residues within 4Å: Chain E: D.249, E.278, E.279, M.424, H.425 Ligands: MN.9 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.249, E:E.279, E:E.279, E:H.425 MN.11: 5 residues within 4Å: Chain F: D.249, E.279, M.424, H.425 Ligands: MN.12 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.249, F:E.279, F:E.279, F:H.425, H2O.26 MN.12: 5 residues within 4Å: Chain F: H.92, D.249, E.278, D.326 Ligands: MN.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.92, F:D.249, F:D.326, F:D.326, H2O.26 MN.13: 5 residues within 4Å: Chain G: H.92, D.249, E.278, D.326 Ligands: MN.14 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.92, G:D.249, G:D.326, G:D.326 MN.14: 6 residues within 4Å: Chain G: D.249, E.278, E.279, M.424, H.425 Ligands: MN.13 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.249, G:E.279, G:E.279, G:H.425 MN.15: 5 residues within 4Å: Chain H: H.92, D.249, E.278, D.326 Ligands: MN.16 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.92, H:D.249, H:D.326, H:D.326, H2O.36 MN.16: 6 residues within 4Å: Chain H: D.249, E.278, E.279, M.424, H.425 Ligands: MN.15 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.249, H:E.279, H:E.279, H:H.425, H2O.36 MN.17: 6 residues within 4Å: Chain I: H.92, D.249, E.278, E.279, D.326 Ligands: MN.18 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.92, I:D.249, I:D.326, I:D.326, H2O.40 MN.18: 6 residues within 4Å: Chain I: D.249, E.278, E.279, M.424, H.425 Ligands: MN.17 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.249, I:E.279, I:E.279, I:H.425 MN.19: 5 residues within 4Å: Chain J: D.249, E.279, M.424, H.425 Ligands: MN.20 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.249, J:E.279, J:E.279, J:H.425, H2O.45 MN.20: 5 residues within 4Å: Chain J: H.92, D.249, E.278, D.326 Ligands: MN.19 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.92, J:D.249, J:D.326, J:D.326, H2O.45 MN.21: 5 residues within 4Å: Chain K: H.92, D.249, E.278, D.326 Ligands: MN.22 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.92, K:D.249, K:D.326, K:D.326 MN.22: 6 residues within 4Å: Chain K: D.249, E.278, E.279, M.424, H.425 Ligands: MN.21 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.249, K:E.279, K:E.279, K:H.425 MN.23: 5 residues within 4Å: Chain L: H.92, D.249, E.278, D.326 Ligands: MN.24 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.92, L:D.249, L:D.326, L:D.326, H2O.54 MN.24: 6 residues within 4Å: Chain L: D.249, E.278, E.279, M.424, H.425 Ligands: MN.23 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.249, L:E.279, L:E.279, L:H.425, H2O.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, T. et al., Crystal structure of Aminipeptidase (M18 family) from Thermotoga Maritima. To be Published

Release Date

2006-06-13

Peptides

Probable M18-family aminopeptidase 1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Probable M18-family aminopeptidase 1