SMTL ID : 3l2n.1

Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: H.185, E.188, H.278 Ligands: UNL.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.185, A:E.188, A:E.188, A:H.278 CA.5: 4 residues within 4Å: Chain B: H.185, E.188, H.278 Ligands: UNL.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.185, B:E.188, B:E.188, B:H.278 CA.8: 4 residues within 4Å: Chain C: H.185, E.188, H.278 Ligands: UNL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.185, C:E.188, C:E.188, C:H.278 CA.12: 4 residues within 4Å: Chain D: H.185, E.188, H.278 Ligands: UNL.13 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.185, D:E.188, D:E.188, D:H.278

4 x UNL: UNKNOWN LIGAND

UNL.2: 8 residues within 4Å: Chain A: H.185, R.236, N.245, R.246, H.278, Y.325, E.354 Ligands: CA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.185, A:R.236, A:N.245, A:R.246, A:R.246, A:E.354, A:E.354 UNL.6: 8 residues within 4Å: Chain B: H.185, E.188, R.236, N.245, R.246, H.278, E.354 Ligands: CA.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.188, B:R.236, B:N.245, B:R.246, B:R.246, B:Y.325 UNL.9: 8 residues within 4Å: Chain C: H.185, R.236, N.245, R.246, H.278, Y.325, E.354 Ligands: CA.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.236, C:N.245, C:R.246, C:R.246, C:Y.325, C:Y.325, C:E.354 UNL.13: 8 residues within 4Å: Chain D: H.185, E.188, R.236, N.245, R.246, H.278, E.354 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.188, D:R.236, D:N.245, D:R.246, D:R.246

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

ACT.3: 8 residues within 4Å: Chain A: D.272, L.304, K.347, C.348, L.349, I.393, G.394, Q.395 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.304 Hydrogen bonds: A:D.272, A:D.272, A:G.394 Salt bridges: A:K.300 ACT.4: 4 residues within 4Å: Chain A: E.53, A.242, N.243, R.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.53, A:N.243 Salt bridges: A:R.255 ACT.10: 8 residues within 4Å: Chain C: D.272, L.304, K.347, C.348, L.349, I.393, G.394, Q.395 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.304 Hydrogen bonds: C:D.272, C:G.394 Salt bridges: C:K.300 ACT.11: 4 residues within 4Å: Chain C: E.53, A.242, N.243, R.255 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.53, C:N.243 Salt bridges: C:R.255

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain B: Q.98, W.100, W.193, P.372, E.373 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.100 GOL.14: 5 residues within 4Å: Chain D: Q.98, W.100, W.193, P.372, E.373 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution. To be published

Release Date

2009-12-29

Peptides

Peptidase M14, carboxypeptidase A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Peptidase M14, carboxypeptidase A