SMTL ID : 5byn.1

Canavalia maritima lectin complexed with synthetic selenoamino acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:Y.12, A:D.19, H2O.1, H2O.1 CA.8: 5 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 Ligands: MN.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.10, B:Y.12, H2O.2, H2O.2

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

MN.2: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:H.24, H2O.1, H2O.1 MN.9: 5 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 Ligands: CA.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:H.24, H2O.2, H2O.2

1 x CD: CADMIUM ION(Non-covalent)

CD.3: 1 residues within 4Å: Chain A: E.87 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.87, A:E.87, H2O.1, H2O.1

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: K.36, R.60, S.76, Y.77, D.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.60, A:D.78

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: S.113, L.126, P.178, V.179, H.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.178, A:H.180 EDO.10: 6 residues within 4Å: Chain B: L.107, N.131, Q.132, D.151, G.152, N.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.107 EDO.11: 3 residues within 4Å: Chain B: D.2, N.216, D.218 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.216

2 x 4WM: (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol(Non-covalent)

4WM.6: 8 residues within 4Å: Chain A: S.110, H.127, V.129, D.192, T.194 Chain B: K.114, K.116, H.121 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.129, A:D.192, A:T.194 Hydrogen bonds: A:S.110, B:K.114 Salt bridges: A:H.127 4WM.7: 14 residues within 4Å: Chain A: K.114, K.116, S.190, D.192 Chain B: H.51, I.52, I.53, T.112, K.114, S.190, F.191, D.192, A.193, T.194 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:K.114, A:K.116, B:H.51, B:I.53, B:I.53, B:T.112, B:K.114 Hydrogen bonds: A:S.190, B:T.112, B:D.192, B:D.192, B:D.192 Salt bridges: A:K.114, B:H.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nobrega, R.B. et al., Canavalia maritima lectin complexed with synthetic selenoamino acid. To Be Published

Release Date

2015-11-18

Peptides

Concanavalin-A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Concanavalin-A