SMTL ID : 1nxd.6 (7 other biounits)

Crystal structure of MnMn Concanavalin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

16 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.110, A:H.127, A:E.192 Water bridges: A:E.192, A:E.192 AZI.2: 2 residues within 4Å: Chain A: H.127 Chain C: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.224, A:S.225, A:T.226 AZI.4: 3 residues within 4Å: Chain A: T.105, E.155, L.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.105, A:N.153 Water bridges: A:D.151, A:D.151 AZI.13: 6 residues within 4Å: Chain B: S.110, F.111, T.112, H.127, E.192, A.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.110, B:T.112, B:H.127 AZI.14: 2 residues within 4Å: Chain B: H.127 Chain D: H.127 No protein-ligand interaction detected (PLIP) AZI.15: 5 residues within 4Å: Chain B: P.222, S.223, G.224, S.225, T.226 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.222, B:G.224, B:S.225, B:T.226 AZI.16: 3 residues within 4Å: Chain B: T.105, E.155, L.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.153 Water bridges: B:E.155, B:E.155 AZI.25: 2 residues within 4Å: Chain C: D.218, S.220 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.218 Water bridges: C:S.220 AZI.26: 4 residues within 4Å: Chain C: K.138, L.140, I.141, Y.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.140 Water bridges: C:L.142 AZI.27: 4 residues within 4Å: Chain C: T.147, T.157, R.158, V.159 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.157, C:R.158, C:R.158, C:V.159 AZI.28: 3 residues within 4Å: Chain C: Y.12, P.13 Ligands: GOL.34 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.12 Water bridges: C:Y.12, C:Y.12 AZI.38: 2 residues within 4Å: Chain D: D.218, S.220 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.220 AZI.39: 4 residues within 4Å: Chain D: K.138, L.140, I.141, Y.176 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.138 Water bridges: D:L.140, D:L.142, D:Y.176, D:Y.176 AZI.40: 4 residues within 4Å: Chain D: T.147, T.157, R.158, V.159 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.147, D:T.157, D:R.158, D:V.159 AZI.41: 3 residues within 4Å: Chain D: Y.12, P.13 Ligands: GOL.47 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.13

8 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.9 MN.29: 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.13, H2O.15 MN.30: 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.14, H2O.17 MN.42: 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.21, H2O.22 MN.43: 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.22, H2O.25

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

NA.7: 3 residues within 4Å: Chain A: L.107, N.131 Chain C: E.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.107 NA.19: 3 residues within 4Å: Chain B: L.107, N.131 Chain D: E.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.107 NA.31: 3 residues within 4Å: Chain A: E.122 Chain C: L.107, N.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.122 NA.44: 3 residues within 4Å: Chain B: E.122 Chain D: L.107, N.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.122

22 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 C: D.139 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: P.86, W.88, N.216, I.217, D.218 Ligand excluded by PLIP 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 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: K.138, L.140, I.141, Y.176 Ligand excluded by PLIP GOL.20: 10 residues within 4Å: Chain B: W.88, S.113, K.114, N.124, A.125, L.126, P.178, V.179, H.180 Chain D: D.139 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain B: N.14, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: P.86, W.88, N.216, I.217, D.218 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain B: Y.54, S.56, K.59, D.80, D.82, I.181, W.182, E.183, A.189 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: K.138, L.140, I.141, Y.176 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: A.1, P.234, D.235, N.237 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain C: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain C: P.13, N.14, T.15, D.16 Ligands: AZI.28 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain A: D.139 Chain C: S.113, N.124, A.125, L.126, P.178, V.179, H.180 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain C: G.144, I.221 Ligands: GOL.37 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain C: Q.143, G.144, S.220, I.221 Ligands: GOL.36 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain D: A.1, P.234, D.235, N.237 Ligand excluded by PLIP GOL.46: 8 residues within 4Å: Chain D: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain D: P.13, N.14, T.15, D.16 Ligands: AZI.41 Ligand excluded by PLIP GOL.48: 8 residues within 4Å: Chain B: D.139 Chain D: S.113, N.124, A.125, L.126, P.178, V.179, H.180 Ligand excluded by PLIP GOL.49: 3 residues within 4Å: Chain D: G.144, I.221 Ligands: GOL.50 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain D: Q.143, G.144, S.220, I.221 Ligands: GOL.49 Ligand excluded by PLIP

Links

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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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

B
3

C
4

D
4

concanavalin A

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