SMTL ID : 4njr.1

Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.236, E.266, H.401 Ligands: ZN.2, CO3.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.236, A:E.266, A:E.266, A:H.401 ZN.2: 8 residues within 4Å: Chain A: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.1, CO3.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.82, A:D.236, A:D.307, A:D.307, H2O.9 ZN.4: 8 residues within 4Å: Chain B: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.5, CO3.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.82, B:D.236, B:D.307, B:D.307, H2O.17 ZN.5: 5 residues within 4Å: Chain B: D.236, E.266, H.401 Ligands: ZN.4, CO3.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.236, B:E.266, B:E.266, B:H.401 ZN.7: 5 residues within 4Å: Chain C: D.236, E.266, H.401 Ligands: ZN.8, CO3.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.236, C:E.266, C:E.266, C:H.401 ZN.8: 8 residues within 4Å: Chain C: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.7, CO3.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.82, C:D.236, C:D.307, C:D.307, H2O.26 ZN.10: 5 residues within 4Å: Chain D: D.236, E.266, H.401 Ligands: ZN.11, CO3.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.236, D:E.266, D:E.266, D:H.401 ZN.11: 8 residues within 4Å: Chain D: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.10, CO3.12 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.82, D:D.236, D:D.307, D:D.307, H2O.34 ZN.13: 5 residues within 4Å: Chain E: D.236, E.266, H.401 Ligands: ZN.14, CO3.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.236, E:E.266, E:E.266, E:H.401 ZN.14: 8 residues within 4Å: Chain E: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.13, CO3.15 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.82, E:D.236, E:D.307, E:D.307, H2O.43 ZN.16: 8 residues within 4Å: Chain F: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.17, CO3.18 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.82, F:D.236, F:D.307, F:D.307, H2O.51 ZN.17: 5 residues within 4Å: Chain F: D.236, E.266, H.401 Ligands: ZN.16, CO3.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.236, F:E.266, F:E.266, F:H.401 ZN.19: 5 residues within 4Å: Chain G: D.236, E.266, H.401 Ligands: ZN.20, CO3.21 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.236, G:E.266, G:E.266, G:H.401 ZN.20: 8 residues within 4Å: Chain G: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.19, CO3.21 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.82, G:D.236, G:D.307, G:D.307, H2O.60 ZN.22: 5 residues within 4Å: Chain H: D.236, E.266, H.401 Ligands: ZN.23, CO3.24 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.236, H:E.266, H:E.266, H:H.401 ZN.23: 8 residues within 4Å: Chain H: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.22, CO3.24 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.82, H:D.236, H:D.307, H:D.307, H2O.68 ZN.25: 5 residues within 4Å: Chain I: D.236, E.266, H.401 Ligands: ZN.26, CO3.27 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.236, I:E.266, I:E.266, I:H.401 ZN.26: 8 residues within 4Å: Chain I: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.25, CO3.27 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.82, I:D.236, I:D.307, I:D.307, H2O.77 ZN.28: 8 residues within 4Å: Chain J: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.29, CO3.30 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.82, J:D.236, J:D.307, J:D.307, H2O.85 ZN.29: 5 residues within 4Å: Chain J: D.236, E.266, H.401 Ligands: ZN.28, CO3.30 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.236, J:E.266, J:E.266, J:H.401 ZN.31: 5 residues within 4Å: Chain K: D.236, E.266, H.401 Ligands: ZN.32, CO3.33 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.236, K:E.266, K:E.266, K:H.401 ZN.32: 8 residues within 4Å: Chain K: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.31, CO3.33 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.82, K:D.236, K:D.307, K:D.307, H2O.94 ZN.34: 5 residues within 4Å: Chain L: D.236, E.266, H.401 Ligands: ZN.35, CO3.36 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.236, L:E.266, L:E.266, L:H.401 ZN.35: 8 residues within 4Å: Chain L: H.82, D.236, N.237, E.265, E.266, D.307 Ligands: ZN.34, CO3.36 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.82, L:D.236, L:D.307, L:D.307, H2O.102

12 x CO3: CARBONATE ION(Non-functional Binders)

CO3.3: 10 residues within 4Å: Chain A: H.82, D.236, E.265, E.266, D.307, M.400, H.401 Chain D: H.156 Ligands: ZN.1, ZN.2 No protein-ligand interaction detected (PLIP) CO3.6: 10 residues within 4Å: Chain B: H.82, D.236, E.265, E.266, D.307, P.380, H.401 Chain K: H.156 Ligands: ZN.4, ZN.5 No protein-ligand interaction detected (PLIP) CO3.9: 9 residues within 4Å: Chain C: H.82, D.236, E.265, E.266, D.307, H.401 Chain F: H.156 Ligands: ZN.7, ZN.8 No protein-ligand interaction detected (PLIP) CO3.12: 9 residues within 4Å: Chain A: H.156 Chain D: H.82, D.236, E.265, E.266, D.307, H.401 Ligands: ZN.10, ZN.11 No protein-ligand interaction detected (PLIP) CO3.15: 10 residues within 4Å: Chain E: H.82, D.236, E.265, E.266, D.307, M.400, H.401 Chain H: H.156 Ligands: ZN.13, ZN.14 No protein-ligand interaction detected (PLIP) CO3.18: 10 residues within 4Å: Chain C: H.156 Chain F: H.82, D.236, E.265, E.266, D.307, P.380, H.401 Ligands: ZN.16, ZN.17 No protein-ligand interaction detected (PLIP) CO3.21: 9 residues within 4Å: Chain G: H.82, D.236, E.265, E.266, D.307, H.401 Chain J: H.156 Ligands: ZN.19, ZN.20 No protein-ligand interaction detected (PLIP) CO3.24: 9 residues within 4Å: Chain E: H.156 Chain H: H.82, D.236, E.265, E.266, D.307, H.401 Ligands: ZN.22, ZN.23 No protein-ligand interaction detected (PLIP) CO3.27: 10 residues within 4Å: Chain I: H.82, D.236, E.265, E.266, D.307, M.400, H.401 Chain L: H.156 Ligands: ZN.25, ZN.26 No protein-ligand interaction detected (PLIP) CO3.30: 10 residues within 4Å: Chain G: H.156 Chain J: H.82, D.236, E.265, E.266, D.307, P.380, H.401 Ligands: ZN.28, ZN.29 No protein-ligand interaction detected (PLIP) CO3.33: 9 residues within 4Å: Chain B: H.156 Chain K: H.82, D.236, E.265, E.266, D.307, H.401 Ligands: ZN.31, ZN.32 No protein-ligand interaction detected (PLIP) CO3.36: 9 residues within 4Å: Chain I: H.156 Chain L: H.82, D.236, E.265, E.266, D.307, H.401 Ligands: ZN.34, ZN.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, D.D. et al., Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa. Biochem.Biophys.Res.Commun. (2014)

Release Date

2014-04-02

Peptides

Probable M18 family aminopeptidase 2: 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 2

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