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- PDB-2cna: THE COVALENT AND THREE-DIMENSIONAL STRUCTURE OF CONCANAVALIN A, I... -

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Database: PDB / ID: 2cna
TitleTHE COVALENT AND THREE-DIMENSIONAL STRUCTURE OF CONCANAVALIN A, IV.ATOMIC COORDINATES,HYDROGEN BONDING,AND QUATERNARY STRUCTURE
ComponentsCONCANAVALIN A
KeywordsLECTIN (AGGLUTININ)
Function / homology
Function and homology information


regulation of defense response to virus / mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsReekejunior, G.N. / Becker, J.W. / Edelman, G.M.
Citation
Journal: J.Biol.Chem. / Year: 1975
Title: The covalent and three-dimensional structure of concanavalin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure.
Authors: Reeke Jr., G.N. / Becker, J.W. / Edelman, G.M.
#1: Journal: J.Biol.Chem. / Year: 1975
Title: The Covalent and Three-Dimensional Structure of Concanavalin A, I.Amino Acid Sequence of Cyanogen Bromide Fragments F1 and F2
Authors: Wang, J.L. / Cunningham, B.A. / Waxdal, M.J. / Edelman, G.M.
#2: Journal: J.Biol.Chem. / Year: 1975
Title: The Covalent and Three-Dimensional Structure of Concanavalin A, II.Amino Acid Sequence of Cyanogen Bromide Fragment F3
Authors: Cunningham, B.A. / Wang, J.L. / Waxdal, M.J. / Edelman, G.M.
#3: Journal: J.Biol.Chem. / Year: 1975
Title: The Covalent and Three-Dimensional Structure of Concanavalin A, III.Structure of the Monomer and its Interactions with Metals and Saccharides
Authors: Becker, J.W. / Reekejunior, G.N. / Wang, J.L. / Cunningham, B.A. / Edelman, G.M.
#4: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#5: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionApr 1, 1975Processing site: BNL
Revision 1.0Mar 16, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE MOLECULE CONTAINS TWO PLEATED SHEET STRUCTURES OF SEVEN ANTIPARALLEL STRANDS EACH. TWO ...SHEET THE MOLECULE CONTAINS TWO PLEATED SHEET STRUCTURES OF SEVEN ANTIPARALLEL STRANDS EACH. TWO STRANDS (5 AND 6) OF THE SHEET DESIGNATED *BK* AND ONE STRAND (6) OF THE SHEET DESIGNATED *FT* CONTAIN RESIDUES FROM DISCONTINUOUS PARTS OF THE AMINO ACID SEQUENCE. IN THE FORMAT SPECIFIED BY THE DATA BANK FOR REPRESENTING SUCH SHEETS ON SHEET CARDS, EACH SHEET IS LISTED TWICE. THE SINGLE *BK* SHEET IS LISTED ONCE AS *BK1* AND ONCE AS *BK2*, AND THE SINGLE *FT* SHEET IS LISTED ONCE AS *FT1* AND ONCE AS *FT2*. THESE REDUNDANT DESCRIPTIONS DO NOT IMPLY THE PRESENCE OF MORE THAN TWO SHEETS IN THE STRUCTURE. STRANDS 1,2,3,4 OF BK1 ARE THE SAME AS STRANDS 1,2,3,4 OF BK2. SIMILARLY, STRANDS 1,2,3, 4,5 OF FT1 ARE THE SAME AS STRANDS 1,2,3,4,5 OF FT2. THE NON-IDENTICAL STRANDS DESCRIBE THE DISJOINT SEGMENTS OF STRANDS 5 AND 6 OF THE *BK* SHEET AND STRAND 6 OF THE *FT* SHEET. IN ORDER TO PRESENT THE PLEATED SHEET STRUCTURE OF CON A IN A MORE EASILY UNDERSTOOD FORMAT, THE FOLLOWING REMARK CARDS CONTAIN A DESCRIPTION OF THE SHEETS LIKE THAT ON THE SHEET CARDS, EXCEPT THAT EACH SHEET IS LISTED ONCE ONLY, AND DISJOINT STRANDS ARE DESIGNATED BY LETTERS, E.G. 5A, 5B ETC. 1 BK 7 THR 73 VAL 79 0 2 BK 7 LYS 59 SER 66 -1 N VAL 75 O ALA 63 3 BK 7 GLY 48 SER 56 -1 N VAL 64 O HIS 51 4 BK 7 VAL 188 LYS 200 -1 N ILE 52 O ALA 193 5A BK 7 SER 108 LYS 116 -1 N GLU 192 O THR 112 5B BK 7 THR 103 ILE 106 -1 N LEU 198 O THR 105 6A BK 7 ASP 124 PHE 130 -1 N SER 113 O LEU 126 6B BK 7 ASN 153 LEU 156 -1 N ILE 106 O LEU 154 7 BK 7 THR 147 GLY 149 -1 N GLU 155 O THR 147 1 FNT 7 LYS 35 TRP 40 0 2 FNT 7 PRO 23 LYS 30 -1 N ALA 38 O ILE 25 3 FNT 7 ILE 4 THR 11 -1 N GLY 26 O GLU 8 4 FNT 7 ASP 208 SER 215 -1 N VAL 7 O PHE 212 5 FNT 7 GLU 87 THR 97 -1 N PHE 213 O GLY 92 6AFNT 7 SER 169 TYR 176 -1 N LEU 93 O ALA 173 6BFNT 7 VAL 179 ILE 181 -1 N VAL 89 O VAL 179 7 FNT 7 ASP 139 GLN 143 -1 N LEU 174 O ILE 141 SEVERAL RESIDUES WITHIN EACH SHEET STRUCTURE HAVE UNUSUAL CONFORMATIONS OR FORM UNUSUAL HYDROGEN BONDS. THESE PECULIARITIES ARE DOCUMENTED IN THE REFERENCES GIVEN. STRAND 6 OF SHEET BK1 HYDROGEN BONDS TO A SYMMETRY-RELATED STRAND IN ANOTHER PROTOMER TO FORM A 12-STRANDED ANTI- PARALLEL SHEET IN THE DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6913
Polymers25,5961
Non-polymers952
Water724
1
A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,76512
Polymers102,3854
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11270 Å2
ΔGint-111 kcal/mol
Surface area32950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.910, 87.230, 63.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: A001 WEAK DENSITY, INTERPRETATION UNCERTAIN / 2: E008 MN2+ LIGAND; OE1 CLOSE TO D28 OD1 / 3: D010 MN2+ AND CA2+ LIGAND
4: T011 OG JOINED TO E102 OE2 & D208 O -PROB BIFURCATED H-BOND
5: Y012 SIDE CHAIN IS NEAR ANOTHER MOLECULE / 6: N014 CA2+ LIGAND / 7: D016 OD1 WEAK / 8: I017 CG2 WEAK / 9: G018 EXTRA DENSITY AT CA; O - MN2+ SOLVENT BRIDGE / 10: D019 MN2+ AND CA2+ LIGAND; O CLOSE TO P20 O / 11: P020 CG, CD WEAK; O CLOSE TO D19 O / 12: Y022 OH WEAK / 13: P023 CARBONYL WEAK / 14: H024 MN2+ LIGAND; SIDE CHAIN STRONG / 15: I025 CD1 WEAK / 16: D028 CLOSE TO E8 OE1 / 17: K030 SIDE CHAIN DISORDERED BEYOND CD / 18: V032 SIDE CHAIN IS MISSHAPEN; W1 IS MN2+ LIGAND / 19: R033 CB, CG WEAK
20: S034 STRONG DENSITY HARD TO INTERPRET; W2 IS MN2+ LIGAND
21: K039 SIDE CHAIN DISORDERED BEYOND CB / 22: W040 CB WEAK / 23: N041 SIDE CHAIN DISORDERED / 24: M042 CA WEAK / 25: D044 CARBONYL WEAK / 26: K046 SIDE CHAIN DISORDERED BEYOND CD / 27: S056 CARBONYL WEAK / 28: D058 DENSITY VERY STRONG; TETRAMER SALT BRIDGE
29: R060 DENSITY CONFUSING AT GUANIDINIUM; TETRAMER SALT BRIDGE
30: P068 ALMOST SPHERICAL / 31: N069 DENSITY SOMEWHAT SPREAD OUT / 32: A072 DENSITY DISTORTED AT CB / 33: T073 NO DENSITY FOR SIDE CHAIN / 34: S076 CARBONYL WEAK / 35: D080 SIDE CHAIN CONFUSING / 36: N082 SIDE CHAIN WEAK / 37: L085 SIDE CHAIN CONFUSING / 38: P086 CG AND CD WEAK / 39: E087 CG WEAK / 40: V089 SIDE CHAIN DISORDERED / 41: A095 PROBABLY IS CLOSER TO G171
42: G098 STRONG BRIDGE G98 N - Y100 O MAKES INTERP DIFFICULT
43: L099 SIDE CHAIN DENSITY ALMOST ABSENT / 44: T105 SIDE CHAIN DISORDERED / 45: S108 OG POSITION UNCLEAR / 46: K114 CD WEAK; TETRAMER SLAT LINK / 47: K116 C, CD WEAK; TETRAMER SLAT LINK / 48: S117 SIDE CHAIN WEAK / 49: S119 DENSITY CONFUSING; INTERPRETATION UNCERTAIN / 50: T120 DENSITY CONFUSING; INTERPRETATION UNCERTAIN / 51: H121 SIDE CHAIN AND CARBONYL WEAK / 52: Q122 N, CB WEAK; LOCAL DISORDER AT 2-FOLD PARALLEL TO X / 53: T123 SIDE CHAIN CONFUSING / 54: H127 LARGE DENSITY AT SITE OF NEARBY METAL SUBSTITUENTS / 55: M129 SIDE CHAIN DENSITY JOINS H127; SEE H127 / 56: Q132 CB WEAK / 57: K135 CARBONYL CONFUSING / 58: D136 SIDE CHAIN DISORDERED / 59: Q137 CONFORMATION PECULIAR; INTERPRETATION UNCERTAIN / 60: A146 CB WEAK / 61: T147 SIDE CHAIN DENSITY CONFUSING / 62: T148 LARGE DENSITY AT CARBONYL; PROBABLE DISORDER / 63: T150 SIDE CHAIN DENSITY NOT IDENTIFIABLE / 64: D151 N WEAK / 65: L154 N WEAK / 66: V159 CG1, CG2 WEAK / 67: S160 SIDE CHAIN CONFUSING; AMIDE H-BOND BIFURCATED / 68: S161 DENSITY CONFUSING / 69: N162 DENSITY CONFUSING; INTERPRETATION UNCERTAIN / 70: E166 SIDE CHAIN DENSITY AT CARBOXYL ONLY / 71: S168 ORIENTATION OF OG UNCLEAR / 72: S169 OG H-BOND BIFURCATED / 73: Y176 CE2 WEAK; CARBONYL STRONG / 74: A177 CARBONYL WEAK; APPEARS OUT OF PLANE OF P178 / 75: H180 O WEAK / 76: I181 CG2 HAS NO DENSITY / 77: S184 SIDE CHAIN DISORDERED; NEAR ANOTHER MOLECULE / 78: S185 SIDE CHAIN CONFUSING / 79: T187 DENSITY CONFUSING - LARGE SIDE CHAIN PRESENT / 80: S189 OG WEAK / 81: E192 TETRAMER SALT LINKS
82: T194 SIDE CHAIN DISORDERED; JOINS H51; AMIDE H-BOND BIFURC?
83: A196 SIDE CHAIN DISORDERED / 84: L198 SIDE CHAIN SLIGHTLY DISORDERED / 85: K200 DISORDERED BEYOND CD / 86: S201 AMIDE H-BOND IS BIFURCATED / 87: A207 POSSIBLE CIS-PEPTIDE / 88: N216 ORIENTATION OF CARBOXAMIDO GROUP UNCERTAIN / 89: S220 PEPTIDE CONFUSING; AMIDE H-BOND BIFURCATED / 90: I221 SIDE CHAIN WEAK / 91: S223 SIDE CHAIN DISORDERED / 92: G224 CARBONYL WEAK / 93: S225 OG DISORDERED / 94: R228 CARBONYL WEAK; GUANIDINIUM GROUP CONFUSING / 95: L230 SIDE CHAIN VERY WEAK BEYOND CB / 96: L232 SIDE CHAIN CONFUSING / 97: F233 CZ WEAK
98: D235 - N237 APPEAR TO EXIST IN 2 CONFORMATIONS- NEITHER FIT IS VERY GOOD; SIDE CHAIN OBSCURE

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Components

#1: Protein CONCANAVALIN A /


Mass: 25596.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALL SEQUENCES OF 4 RESIDUES FOR WHICH THE DISTANCE CA(I)-CA (I+3) IS LESS THAN 7 ANGSTROMS ARE ...ALL SEQUENCES OF 4 RESIDUES FOR WHICH THE DISTANCE CA(I)-CA (I+3) IS LESS THAN 7 ANGSTROMS ARE LISTED BELOW IN THE TURN RECORDS. THOSE TURNS WHICH PROBABLY CONTAIN THE HYDROGEN BOND N(I+3)...O(I) ARE DESIGNATED AS TYPE I OR TYPE II *BETA-BENDS* IN THE LISTING BELOW.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal grow
*PLUS
pH: 6.8 / Method: unknown / Details: referred to J.Biol.Chem. 250.1513-1524 1975
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.10 M11Na2SO4
20.01 Msodium maleate11

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Processing

RefinementHighest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 2 4 1813
Refinement
*PLUS
Num. reflection obs: 10221 / Rfactor obs: 0.411
Solvent computation
*PLUS
Displacement parameters
*PLUS

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