university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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3l2f
TRANSFERASE HEADER
GLYCOCYAMINE KINASE, BETA-BETA HOMODIMER FROM MARINE WORM NAMALYCASTIS SP., WITH TRANSITION STATE ANALOG MG(II)-ADP- NO3-GLYCOCYAMINE. PART 1. TITLE
GLYCOCYAMINE KINASE BETA CHAIN COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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NMG B 502
82B LYS
83B LYS
84B THR
212B LEU
243B GLU
294B CYS
296B THR
331B ARG
336B GLU
NMG E 505
82E LYS
83E LYS
84E THR
85E GLY
212E LEU
243E GLU
294E CYS
296E THR
297E ASN
331E ARG
336E GLU
NMG C 503
82C LYS
83C LYS
84C THR
85C GLY
212C LEU
243C GLU
294C CYS
296C THR
297C ASN
331C ARG
336C GLU
NMG H 508
82H LYS
83H LYS
84H THR
85H GLY
212H LEU
243H GLU
294H CYS
296H THR
297H ASN
331H ARG
336H GLU
352H ARG
NMG R 518
82R LYS
83R LYS
84R THR
85R GLY
212R LEU
243R GLU
294R CYS
296R THR
297R ASN
331R ARG
336R GLU
350R TRP
NMG I 509
82I LYS
83I LYS
84I THR
85I GLY
212I LEU
243I GLU
294I CYS
296I THR
297I ASN
331I ARG
336I GLU
NMG O 515
82O LYS
83O LYS
84O THR
85O GLY
212O LEU
243O GLU
294O CYS
296O THR
297O ASN
331O ARG
336O GLU
NMG P 516
82P LYS
83P LYS
84P THR
212P LEU
243P GLU
294P CYS
296P THR
331P ARG
336P GLU
350P TRP
NMG D 504
82D LYS
83D LYS
84D THR
85D GLY
212D LEU
243D GLU
294D CYS
296D THR
297D ASN
331D ARG
336D GLU
350D TRP
NMG J 510
82J LYS
83J LYS
84J THR
212J LEU
243J GLU
294J CYS
296J THR
297J ASN
331J ARG
336J GLU
350J TRP
352J ARG
NMG Q 517
82Q LYS
83Q LYS
84Q THR
85Q GLY
212Q LEU
243Q GLU
294Q CYS
296Q THR
297Q ASN
331Q ARG
336Q GLU
350Q TRP
NMG A 501
82A LYS
83A LYS
84A THR
85A GLY
212A LEU
243A GLU
294A CYS
296A THR
297A ASN
331A ARG
336A GLU
NMG G 507
82G LYS
83G LYS
84G THR
212G LEU
243G GLU
294G CYS
296G THR
297G ASN
331G ARG
336G GLU
350G TRP
352G ARG
NMG M 513
82M LYS
83M LYS
84M THR
85M GLY
212M LEU
243M GLU
294M CYS
296M THR
297M ASN
331M ARG
336M GLU
350M TRP
NMG F 506
82F LYS
83F LYS
84F THR
85F GLY
212F LEU
243F GLU
294F CYS
296F THR
297F ASN
331F ARG
336F GLU
350F TRP
352F ARG
NMG K 511
82K LYS
83K LYS
84K THR
212K LEU
243K GLU
294K CYS
296K THR
297K ASN
331K ARG
336K GLU
350K TRP
352K ARG
NMG L 512
82L LYS
83L LYS
84L THR
85L GLY
212L LEU
243L GLU
294L CYS
296L THR
297L ASN
331L ARG
336L GLU
NMG N 514
82N LYS
83N LYS
84N THR
85N GLY
212N LEU
243N GLU
294N CYS
296N THR
297N ASN
331N ARG
336N GLU
350N TRP
ADP B 602
139B SER
140B CYS
141B ARG
143B ARG
199B ILE
202B HIS
204B LEU
205B PHE
206B GLU
239B TRP
247B ARG
251B MET
303B ARG
305B SER
306B VAL
307B HIS
331B ARG
333B THR
334B GLY
335B GLY
336B GLU
346B ASP
ADP E 605
139E SER
140E CYS
141E ARG
143E ARG
199E ILE
202E HIS
204E LEU
205E PHE
206E GLU
239E TRP
247E ARG
251E MET
303E ARG
305E SER
306E VAL
307E HIS
331E ARG
333E THR
334E GLY
335E GLY
336E GLU
337E SER
346E ASP
ADP C 603
139C SER
140C CYS
141C ARG
143C ARG
199C ILE
202C HIS
204C LEU
205C PHE
206C GLU
239C TRP
247C ARG
251C MET
303C ARG
305C SER
306C VAL
307C HIS
331C ARG
333C THR
334C GLY
335C GLY
336C GLU
337C SER
346C ASP
ADP H 608
139H SER
140H CYS
141H ARG
143H ARG
199H ILE
202H HIS
204H LEU
205H PHE
239H TRP
247H ARG
251H MET
303H ARG
305H SER
306H VAL
307H HIS
331H ARG
333H THR
334H GLY
335H GLY
336H GLU
346H ASP
ADP R 618
139R SER
140R CYS
141R ARG
143R ARG
199R ILE
202R HIS
204R LEU
205R PHE
206R GLU
239R TRP
247R ARG
251R MET
303R ARG
305R SER
306R VAL
307R HIS
331R ARG
333R THR
334R GLY
335R GLY
336R GLU
346R ASP
ADP I 609
139I SER
140I CYS
141I ARG
143I ARG
199I ILE
202I HIS
204I LEU
206I GLU
239I TRP
247I ARG
251I MET
303I ARG
305I SER
306I VAL
307I HIS
331I ARG
333I THR
334I GLY
335I GLY
336I GLU
337I SER
346I ASP
ADP O 615
139O SER
140O CYS
141O ARG
143O ARG
199O ILE
202O HIS
204O LEU
205O PHE
206O GLU
239O TRP
247O ARG
251O MET
303O ARG
305O SER
306O VAL
307O HIS
331O ARG
333O THR
334O GLY
335O GLY
336O GLU
346O ASP
ADP P 616
139P SER
140P CYS
141P ARG
143P ARG
199P ILE
202P HIS
204P LEU
205P PHE
206P GLU
239P TRP
247P ARG
251P MET
303P ARG
305P SER
307P HIS
331P ARG
333P THR
334P GLY
335P GLY
336P GLU
337P SER
346P ASP
ADP D 604
139D SER
140D CYS
141D ARG
143D ARG
199D ILE
202D HIS
204D LEU
205D PHE
206D GLU
239D TRP
247D ARG
251D MET
303D ARG
305D SER
306D VAL
307D HIS
331D ARG
333D THR
334D GLY
335D GLY
336D GLU
346D ASP
ADP J 610
139J SER
140J CYS
141J ARG
143J ARG
199J ILE
202J HIS
204J LEU
239J TRP
247J ARG
251J MET
303J ARG
305J SER
306J VAL
307J HIS
331J ARG
333J THR
334J GLY
335J GLY
336J GLU
337J SER
346J ASP
ADP Q 617
139Q SER
140Q CYS
141Q ARG
143Q ARG
199Q ILE
202Q HIS
204Q LEU
205Q PHE
206Q GLU
239Q TRP
247Q ARG
251Q MET
303Q ARG
305Q SER
306Q VAL
307Q HIS
331Q ARG
333Q THR
334Q GLY
335Q GLY
336Q GLU
346Q ASP
ADP A 601
139A SER
140A CYS
141A ARG
143A ARG
199A ILE
202A HIS
204A LEU
205A PHE
206A GLU
239A TRP
247A ARG
251A MET
303A ARG
305A SER
306A VAL
307A HIS
331A ARG
333A THR
334A GLY
335A GLY
336A GLU
337A SER
346A ASP
ADP G 607
139G SER
140G CYS
141G ARG
143G ARG
199G ILE
202G HIS
204G LEU
205G PHE
239G TRP
247G ARG
251G MET
303G ARG
305G SER
306G VAL
307G HIS
331G ARG
333G THR
334G GLY
335G GLY
336G GLU
346G ASP
ADP M 613
139M SER
140M CYS
141M ARG
143M ARG
199M ILE
202M HIS
204M LEU
205M PHE
206M GLU
239M TRP
247M ARG
251M MET
303M ARG
305M SER
306M VAL
307M HIS
331M ARG
333M THR
334M GLY
335M GLY
336M GLU
346M ASP
ADP F 606
139F SER
140F CYS
141F ARG
143F ARG
199F ILE
202F HIS
204F LEU
205F PHE
239F TRP
247F ARG
251F MET
252F GLN
303F ARG
305F SER
306F VAL
307F HIS
331F ARG
333F THR
334F GLY
335F GLY
336F GLU
346F ASP
ADP K 611
139K SER
140K CYS
141K ARG
143K ARG
199K ILE
202K HIS
204K LEU
205K PHE
239K TRP
247K ARG
251K MET
303K ARG
305K SER
306K VAL
307K HIS
331K ARG
333K THR
334K GLY
335K GLY
336K GLU
346K ASP
ADP L 612
139L SER
140L CYS
141L ARG
143L ARG
199L ILE
202L HIS
204L LEU
205L PHE
206L GLU
239L TRP
247L ARG
251L MET
303L ARG
305L SER
307L HIS
331L ARG
333L THR
334L GLY
335L GLY
336L GLU
346L ASP
ADP N 614
139N SER
140N CYS
141N ARG
143N ARG
199N ILE
202N HIS
204N LEU
205N PHE
239N TRP
247N ARG
251N MET
303N ARG
305N SER
306N VAL
307N HIS
331N ARG
333N THR
334N GLY
335N GLY
336N GLU
346N ASP
NO3 B 802
143B ARG
243B GLU
247B ARG
296B THR
297B ASN
331B ARG
336B GLU
352B ARG
NO3 E 805
143E ARG
243E GLU
247E ARG
296E THR
297E ASN
331E ARG
336E GLU
352E ARG
NO3 C 803
143C ARG
243C GLU
247C ARG
296C THR
297C ASN
331C ARG
336C GLU
352C ARG
NO3 H 808
143H ARG
242H GLU
243H GLU
247H ARG
296H THR
297H ASN
331H ARG
336H GLU
352H ARG
NO3 R 818
143R ARG
242R GLU
243R GLU
247R ARG
296R THR
297R ASN
331R ARG
336R GLU
352R ARG
NO3 I 809
143I ARG
243I GLU
247I ARG
297I ASN
331I ARG
336I GLU
352I ARG
NO3 O 815
143O ARG
243O GLU
247O ARG
296O THR
297O ASN
331O ARG
336O GLU
352O ARG
NO3 P 816
143P ARG
243P GLU
247P ARG
296P THR
297P ASN
331P ARG
336P GLU
352P ARG
NO3 D 804
143D ARG
243D GLU
247D ARG
296D THR
297D ASN
331D ARG
336D GLU
352D ARG
NO3 J 810
143J ARG
243J GLU
247J ARG
296J THR
297J ASN
331J ARG
336J GLU
352J ARG
NO3 Q 817
143Q ARG
243Q GLU
247Q ARG
296Q THR
297Q ASN
331Q ARG
336Q GLU
352Q ARG
NO3 A 801
143A ARG
243A GLU
247A ARG
296A THR
297A ASN
331A ARG
336A GLU
352A ARG
NO3 G 807
143G ARG
243G GLU
247G ARG
296G THR
297G ASN
331G ARG
336G GLU
352G ARG
NO3 M 813
143M ARG
243M GLU
247M ARG
296M THR
297M ASN
331M ARG
336M GLU
352M ARG
NO3 F 806
143F ARG
243F GLU
247F ARG
297F ASN
331F ARG
336F GLU
352F ARG
NO3 K 811
143K ARG
243K GLU
247K ARG
296K THR
297K ASN
331K ARG
336K GLU
352K ARG
NO3 L 812
143L ARG
243L GLU
247L ARG
296L THR
297L ASN
331L ARG
336L GLU
352L ARG
NO3 N 814
143N ARG
243N GLU
247N ARG
296N THR
297N ASN
331N ARG
336N GLU
352N ARG
MG B 702
239B TRP
242B GLU
243B GLU
247B ARG
336B GLU
MG E 705
239E TRP
242E GLU
243E GLU
247E ARG
336E GLU
MG C 703
239C TRP
242C GLU
243C GLU
247C ARG
336C GLU
MG H 708
239H TRP
242H GLU
243H GLU
247H ARG
336H GLU
MG R 718
239R TRP
242R GLU
243R GLU
336R GLU
MG I 709
239I TRP
242I GLU
243I GLU
247I ARG
MG O 715
239O TRP
242O GLU
243O GLU
247O ARG
336O GLU
MG P 716
239P TRP
242P GLU
243P GLU
247P ARG
336P GLU
MG D 704
239D TRP
242D GLU
243D GLU
247D ARG
MG J 710
239J TRP
242J GLU
243J GLU
247J ARG
336J GLU
MG Q 717
239Q TRP
242Q GLU
243Q GLU
247Q ARG
336Q GLU
MG A 701
239A TRP
242A GLU
243A GLU
247A ARG
336A GLU
MG G 707
239G TRP
242G GLU
243G GLU
336G GLU
MG M 713
239M TRP
242M GLU
243M GLU
247M ARG
336M GLU
MG F 706
239F TRP
242F GLU
243F GLU
336F GLU
MG K 711
239K TRP
242K GLU
243K GLU
247K ARG
336K GLU
MG L 712
239L TRP
242L GLU
243L GLU
247L ARG
336L GLU
MG N 714
239N TRP
242N GLU
243N GLU
247N ARG
336N GLU
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
3l2d Details
other holo-structures
pdb ID Ligand Unique ID
3l2g ADPB_618 NMGD_518 NO3E_818 _MGC_718 Details
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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ADP NAME: ADENOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O10 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
NMG NAME: GUANIDINO ACETATE
FORMULA: C3 H7 N3 O2
SMILES: NC(=N)NCC(O)=O
NO3 NAME: NITRATE ION
FORMULA: N1 O3
SMILES: [O-][N+]([O-])=O
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
Script execution time: 2.3071 seconds