SMTL ID : 1nxd.7 (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: 4 residues within 4Å: Chain A: T.103, T.105, E.155, L.198 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.103, A:T.105, A:T.105, A:E.155, A:E.155 Water bridges: A:N.153, A:N.153 AZI.2: 7 residues within 4Å: Chain A: S.113, K.114, H.180, I.181, S.190, F.191 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.114, A:K.114, A:K.114, A:S.190, A:S.190 AZI.3: 7 residues within 4Å: Chain A: S.110, F.111, T.112, H.127, E.192, A.193, T.194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.112, A:H.127, A:E.192, A:E.192, A:T.194 AZI.15: 2 residues within 4Å: Chain A: H.127 Chain B: H.127 No protein-ligand interaction detected (PLIP) AZI.16: 4 residues within 4Å: Chain B: K.138, L.140, I.141, Y.176 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.138 Water bridges: B:Q.137, B:L.140, B:L.140, B:L.142 AZI.17: 3 residues within 4Å: Chain B: Y.12, P.13, H.205 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.12, B:P.13, B:H.205 Water bridges: B:Y.12, B:Y.12 AZI.18: 7 residues within 4Å: Chain A: W.88, N.124, H.180 Chain B: F.130, Q.137, D.139 Ligands: GOL.10 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.124, A:H.180, B:Q.137, B:Q.137, B:D.139 Water bridges: B:Q.132, B:Q.137 AZI.19: 5 residues within 4Å: Chain B: T.103, T.105, E.155, L.198, K.200 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.103, B:T.103, B:T.105, B:T.105, B:K.200

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

MN.4: 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.2499, H2O.2499 MN.5: 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.2500, H2O.2500 MN.20: 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.2460, H2O.2460 MN.21: 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.2461, H2O.2461

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

NA.6: 3 residues within 4Å: Chain A: L.107, N.131 Chain B: E.122 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.107 Water bridges: B:E.122 NA.22: 3 residues within 4Å: Chain B: L.107, N.131, N.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.107

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: N.44, S.201, D.203, S.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.44 GOL.8: 4 residues within 4Å: Chain A: A.1, P.222, S.223, P.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.223, A:S.223, A:P.234 GOL.9: 8 residues within 4Å: Chain A: Y.12, N.14, G.98, L.99, Y.100, A.207, D.208, R.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.14, A:L.99, A:Y.100, A:Y.100, A:D.208, A:R.228 GOL.10: 10 residues within 4Å: Chain A: S.113, N.124, A.125, L.126, V.179, H.180 Chain B: M.129, D.139 Ligands: AZI.2, AZI.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.113, A:S.113, A:H.180 GOL.11: 5 residues within 4Å: Chain A: Y.12, P.13, N.14, T.15, D.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.15, A:T.15, A:D.16, A:D.16 GOL.12: 4 residues within 4Å: Chain A: Q.143, G.144, S.220, I.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.144, A:I.221 Water bridges: A:Q.143 GOL.13: 4 residues within 4Å: Chain A: A.38, S.72, A.73, T.74 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.74 Water bridges: A:K.39, A:S.72, A:S.72, A:T.74 GOL.14: 5 residues within 4Å: Chain A: K.138, L.140, I.141, Y.176 Chain B: P.178 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.136, A:L.142 GOL.23: 5 residues within 4Å: Chain B: A.38, K.39, S.72, A.73, T.74 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.39, B:K.39, B:T.74 GOL.24: 10 residues within 4Å: Chain A: D.139 Chain B: S.113, K.114, L.115, N.124, A.125, L.126, P.178, V.179, H.180 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: B:P.178, B:H.180 Water bridges: A:D.139, B:N.124 GOL.25: 11 residues within 4Å: Chain B: Y.12, N.14, T.97, G.98, L.99, Y.100, A.207, D.208, G.227, R.228 Ligands: GOL.26 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.14, B:N.14, B:G.98, B:L.99, B:Y.100, B:Y.100, B:R.228 GOL.26: 3 residues within 4Å: Chain B: Y.12, L.99 Ligands: GOL.25 No protein-ligand interaction detected (PLIP) GOL.27: 4 residues within 4Å: Chain B: Q.143, G.144, S.220, I.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.143, B:Q.143, B:G.144, B:I.221 GOL.28: 5 residues within 4Å: Chain B: R.228, L.229, P.234, D.235, A.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.228, B:R.228, B:A.236

Links

RCSB   PDBe   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)

Peptides

concanavalin A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

concanavalin A

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