SMTL ID : 3kgq.1

Carboxypeptidase A liganded to an organic small-molecule: conformational changes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.69, E.72, H.196 Ligands: CIT.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:E.72, A:E.72, A:H.196

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: T.14, L.15, A.117, H.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.15 Water bridges: A:T.14, A:D.16

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 13 residues within 4Å: Chain A: H.69, E.72, R.127, N.144, R.145, H.196, S.197, I.243, I.247, Y.248, A.250, E.270 Ligands: ZN.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.247, A:Y.248 Hydrogen bonds: A:N.144, A:S.197, A:Y.248, A:E.270 Water bridges: A:R.127, A:T.268 Salt bridges: A:H.69, A:H.69, A:R.127, A:R.127, A:R.145, A:R.145, A:H.196, A:H.196

1 x ACN: ACETONE(Non-covalent)

ACN.4: 2 residues within 4Å: Chain A: Q.37, R.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.37, A:R.40

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 3 residues within 4Å: Chain A: I.244, T.245, I.247 No protein-ligand interaction detected (PLIP) FMT.6: 5 residues within 4Å: Chain A: S.199, Q.200, L.201, S.237, K.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.237, A:K.239 FMT.7: 2 residues within 4Å: Chain A: Y.206, Y.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.208 Water bridges: A:Y.206

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: V.183, K.184, G.187, N.188, F.189, Q.261, I.263 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.183, A:G.187, A:F.189, A:F.189, A:Q.261 Water bridges: A:K.190 GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: Y.9, W.81, K.84, K.85, E.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.88 GOL.11: 2 residues within 4Å: Chain A: E.43 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.130 GOL.12: 3 residues within 4Å: Chain A: E.43, G.44 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.43 GOL.13: 6 residues within 4Å: Chain A: Y.12, W.73, R.124, F.279, L.280, L.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.124, A:R.124, A:L.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez, D. et al., Structural and Functional Analysis of the Complex between Citrate and the Zinc Peptidase Carboxypeptidase A. Enzyme Res (2011)

Release Date

2010-10-27

Peptides

Carboxypeptidase A1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carboxypeptidase A1

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