SMTL ID : 1nxd.8 (7 other biounits)

Crystal structure of MnMn Concanavalin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

8 x AZI: AZIDE ION(Non-covalent)

AZI.1: 6 residues within 4Å: Chain A: S.110, F.111, T.112, H.127, E.192, A.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.111, A:H.127 Water bridges: A:E.192, A:E.192 AZI.2: 2 residues within 4Å: Chain A: H.127 Chain B: H.127 No protein-ligand interaction detected (PLIP) AZI.3: 5 residues within 4Å: Chain A: P.222, S.223, G.224, S.225, T.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.222, A:G.224, A:S.225, A:T.226 Water bridges: A:T.226 AZI.4: 3 residues within 4Å: Chain A: T.105, E.155, L.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.105, A:T.105, A:N.153 Water bridges: A:D.151, A:D.151 AZI.13: 2 residues within 4Å: Chain B: D.218, S.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.220 Water bridges: B:S.220 AZI.14: 4 residues within 4Å: Chain B: K.138, L.140, I.141, Y.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.140 Water bridges: B:L.142 AZI.15: 4 residues within 4Å: Chain B: T.147, T.157, R.158, V.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.158, B:R.158, B:V.159, B:V.159 AZI.16: 3 residues within 4Å: Chain B: Y.12, P.13 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.12 Water bridges: B:Y.12, B:Y.12

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

MN.5: 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 MN.6: 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.1, H2O.3 MN.17: 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.7, H2O.8 MN.18: 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.8, H2O.11

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

NA.7: 3 residues within 4Å: Chain A: L.107, N.131 Chain B: E.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.122 NA.19: 3 residues within 4Å: Chain A: E.122 Chain B: L.107, N.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.122

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: W.88, S.113, K.114, N.124, A.125, L.126, P.178, V.179, H.180 Chain B: D.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.178, A:H.180 GOL.9: 8 residues within 4Å: Chain A: N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:G.98, A:L.99, A:Y.100, A:Y.100 Water bridges: A:R.228 GOL.10: 5 residues within 4Å: Chain A: P.86, W.88, N.216, I.217, D.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.217 GOL.11: 9 residues within 4Å: Chain A: Y.54, S.56, K.59, D.80, D.82, I.181, W.182, E.183, A.189 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.54, A:K.59, A:K.59, A:D.82, A:E.183 Water bridges: A:S.56, A:I.181 GOL.12: 4 residues within 4Å: Chain A: K.138, L.140, I.141, Y.176 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.136, A:L.142 GOL.20: 4 residues within 4Å: Chain B: A.1, P.234, D.235, N.237 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.2, B:D.2, B:D.235 GOL.21: 8 residues within 4Å: Chain B: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100 GOL.22: 5 residues within 4Å: Chain B: P.13, N.14, T.15, D.16 Ligands: AZI.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.13, B:T.15, B:D.16 Water bridges: B:T.15 GOL.23: 8 residues within 4Å: Chain A: D.139 Chain B: S.113, N.124, A.125, L.126, P.178, V.179, H.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.124, B:H.180, B:H.180 Water bridges: B:N.124 GOL.24: 3 residues within 4Å: Chain B: G.144, I.221 Ligands: GOL.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.144 GOL.25: 5 residues within 4Å: Chain B: Q.143, G.144, S.220, I.221 Ligands: GOL.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.143, B:Q.143, B:G.144, B:I.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Jaramillo, F.J. et al., Structure of concanavalin A at pH 8: bound solvent and crystal contacts. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-03-30

Peptides

concanavalin A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

B
4

concanavalin A

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