SMTL ID : 5o6n.1

High pressure flash cooled concanavalin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

4 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.5, H2O.6 CA.6: 4 residues within 4Å: Chain B: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:Y.12, B:D.19, H2O.21, H2O.23 CA.11: 4 residues within 4Å: Chain C: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:Y.12, C:D.19, H2O.38, H2O.40 CA.16: 4 residues within 4Å: Chain D: D.10, Y.12, N.14, D.19 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:Y.12, D:D.19, H2O.54, H2O.56

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

MN.2: 4 residues within 4Å: Chain A: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.10, A:D.19, A:H.24, H2O.3, H2O.3 MN.7: 4 residues within 4Å: Chain B: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.10, B:D.19, B:H.24, H2O.19, H2O.20 MN.12: 4 residues within 4Å: Chain C: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.8, C:D.10, C:D.19, C:H.24, H2O.36, H2O.37 MN.17: 4 residues within 4Å: Chain D: E.8, D.10, D.19, H.24 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.8, D:D.10, D:D.19, D:H.24, H2O.53, H2O.53

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

NA.3: 6 residues within 4Å: Chain A: M.42, Q.43, K.46, Y.67, F.197, I.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.46, A:K.46, A:Y.67, A:I.199 NA.8: 6 residues within 4Å: Chain B: M.42, Q.43, K.46, Y.67, F.197, I.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.43, B:K.46, B:Y.67, B:I.199 NA.13: 6 residues within 4Å: Chain C: M.42, Q.43, K.46, Y.67, F.197, I.199 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.46, C:K.46, C:I.199 NA.18: 6 residues within 4Å: Chain D: M.42, Q.43, K.46, Y.67, F.197, I.199 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.46, D:I.199, D:I.199

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: W.40, V.65, S.66, Y.67 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: P.13, H.205 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: W.40, V.65, S.66, Y.67 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: P.13, H.205 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: W.40, V.65, S.66, Y.67 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: P.13, H.205 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain D: W.40, V.65, S.66, Y.67 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain D: P.13, H.205 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quirnheim Pais, D. et al., A standardized technique for high-pressure cooling of protein crystals. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-12-13

Peptides

Concanavalin-A,Concanavalin-A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Concanavalin-A,Concanavalin-A

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