5lyw

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 6-((R)-2-o-Tolyloxymethyl-pyrrolidin-1-yl)-9H-purine

Method: X-RAY DIFFRACTION D_max: 67.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methionine aminopeptidase 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 108–478	Fragment：108-478 Mutation：none	7BH 6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；24% methanol, 100 mM citrate	Resolution 1.69 Å R-free 0.193

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5LYW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B59 COMPLEX OF HUMAN METHIONINE AMINOPEPTIDASE-2 COMPLEXED WITH OVALICIN Deposited 1999-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 109–478（370 aa）	Not recorded	CO COBALT (II) ION × 2 OVA 3,4-DIHYDROXY-2-METHOXY-4-METHYL-3-[2-METHYL-3-(3-METHYL-BUT-2-ENYL) -OXIRANYL]-CYCLOHEXANONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；15-30% T-BUTANOL, 50MM CITRATE BUFFER PH=5.2-5.4	Resolution 1.80 Å R-free 0.222
1B6A HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH TNP-470 Deposited 1999-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–478（478 aa）	Not recorded	CO COBALT (II) ION × 2 TN4 (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.40	Resolution 1.60 Å R-free 0.216
1BN5 HUMAN METHIONINE AMINOPEPTIDASE 2 Deposited 1998-07-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–478（478 aa）	Not recorded	CO COBALT (II) ION × 2 TBU TERTIARY-BUTYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.80 Å R-free 0.228
1BOA HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH ANGIOGENESIS INHIBITOR FUMAGILLIN Deposited 1998-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–478（478 aa）	Not recorded	CO COBALT (II) ION × 2 FUG FUMAGILLIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.80 Å R-free 0.232
1KQ0 Human methionine aminopeptidase type II in complex with D-methionine Deposited 2002-01-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–478（478 aa）	Not recorded	ZN ZINC ION × 2 MED D-METHIONINE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5	Resolution 2.00 Å R-free 0.218
1KQ9 Human methionine aminopeptidase type II in complex with L-methionine Deposited 2002-01-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–478（478 aa）	Not recorded	ZN ZINC ION × 2 MET METHIONINE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5	Resolution 1.90 Å R-free 0.207
1QZY Human Methionine Aminopeptidase in complex with bengamide inhibitor LAF153 and cobalt Deposited 2003-09-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–478（478 aa）	Not recorded	CO COBALT (II) ION × 2 TDE (E)-(2R,3R,4S,5R)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-NON-6-ENOIC ACID ((3S,6R)-6-HYDROXY-2-OXO-AZEPAN-3-YL)-AMIDE × 1 TBU TERTIARY-BUTYL ALCOHOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.211
1R58 Crystal Structure of MetAP2 complexed with A357300 Deposited 2003-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa） Fragment：residues 110-478	Not recorded	MN MANGANESE (II) ION × 2 AO5 N'-((2S,3R)-3-AMINO-2-HYDROXY-5-(ISOPROPYLSULFANYL)PENTANOYL)-N-3-CHLOROBENZOYL HYDRAZIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；isopropyl alcohol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.247
1R5G Crystal Structure of MetAP2 complexed with A311263 Deposited 2003-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa） Fragment：residues 110-478	Not recorded	MN MANGANESE (II) ION × 2 AO1 (2S,3R)-3-AMINO-2-HYDROXY-5-(ETHYLSULFANYL)PENTANOYL-((S)-(-)-(1-NAPHTHYL)ETHYL)AMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.259
1R5H Crystal Structure of MetAP2 complexed with A320282 Deposited 2003-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa） Fragment：residues 110-478	Not recorded	MN MANGANESE (II) ION × 2 AO2 N'-(2S,3R)-3-AMINO-4-CYCLOHEXYL-2-HYDROXY-BUTANO-N-(4-METHYLPHENYL)HYDRAZIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.248
1YW7 h-MetAP2 complexed with A444148 Deposited 2005-02-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa）	Not recorded	MN MANGANESE (II) ION × 2 A41 5-METHYL-2-[(PHENYLSULFONYL)AMINO]BENZOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.85 Å R-free 0.248
1YW8 h-MetAP2 complexed with A751277 Deposited 2005-02-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa）	Not recorded	MN MANGANESE (II) ION × 2 A75 2-[(PHENYLSULFONYL)AMINO]-5,6,7,8-TETRAHYDRONAPHTHALENE-1-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.65 Å R-free 0.273
1YW9 h-MetAP2 complexed with A849519 Deposited 2005-02-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa）	Not recorded	MN MANGANESE (II) ION × 2 A84 2-[({2-[(1Z)-3-(DIMETHYLAMINO)PROP-1-ENYL]-4-FLUOROPHENYL}SULFONYL)AMINO]-5,6,7,8-TETRAHYDRONAPHTHALENE-1-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.64 Å R-free 0.246
2ADU Human Methionine Aminopeptidase Complex with 4-Aryl-1,2,3-triazole Inhibitor Deposited 2005-07-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa） Fragment：residues 110-478	Mutation：V347I	CO COBALT (II) ION × 2 R20 4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；274 K；100 MM CITRATE BUFFER, 30% BUTANOL, pH 5.4, VAPOR DIFFUSION, temperature 274 K, pH 5.40	Resolution 1.90 Å R-free 0.355
2EA2 h-MetAP2 complexed with A773812 Deposited 2007-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa） Fragment：residues 110-478	Not recorded	MN MANGANESE (II) ION × 2 F77 3-ETHYL-6-{[(4-FLUOROPHENYL)SULFONYL]AMINO}-2-METHYLBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20-30 % isopropanol, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.255
2EA4 h-MetAP2 complexed with A797859 Deposited 2007-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa） Fragment：residues 110-478	Not recorded	MN MANGANESE (II) ION × 2 F79 2-(2-AMINOETHOXY)-3-ETHYL-6-{[(4-FLUOROPHENYL)SULFONYL]AMINO}BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20-30 % isopropanol, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.272
2GA2 h-MetAP2 complexed with A193400 Deposited 2006-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa）	Not recorded	MN MANGANESE (II) ION × 2 A19 5-BROMO-2-{[(4-CHLOROPHENYL)SULFONYL]AMINO}BENZOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å R-free 0.251
2OAZ Human Methionine Aminopeptidase-2 Complexed with SB-587094 Deposited 2006-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–478（369 aa）	Not recorded	CO COBALT (II) ION × 2 I96 N-(2-ISOPROPYLPHENYL)-3-[(2-THIENYLMETHYL)THIO]-1H-1,2,4-TRIAZOL-5-AMINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.287
5CLS Structure of human methionine aminopeptidase-2 complexed with spiroepoxytriazole inhibitor (+)-31a Deposited 2015-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa） Fragment：UNP residues 108-478	Not recorded	CO COBALT (II) ION × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 2 52T (4R,7R)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate × 1 CIT CITRIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；292 K；Na Citrate, Tert-butanol	Resolution 1.75 Å R-free 0.189
5D6E Structure of human methionine aminopeptidase 2 with covalent spiroepoxytriazole inhibitor (-)-31b Deposited 2015-08-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa） Fragment：UNP residues 108-478	Not recorded	94A (4R,7S)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate × 1 CO COBALT (II) ION × 2 TBU TERTIARY-BUTYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；Na Citrate, Tert-butanol	Resolution 1.49 Å R-free 0.156
5D6F Structure of human methionine aminopeptidase-2 complexed with spiroepoxytriazole inhibitor (+)-31b Deposited 2015-08-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	57R (4S,7R)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate × 1 CO COBALT (II) ION × 1 TBU TERTIARY-BUTYL ALCOHOL × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；292 K；Na Citrate, Tert-butanol	Resolution 1.55 Å R-free 0.185
5JFR Potent, Reversible MetAP2 Inhibitors via Fragment Based Drug Discovery Deposited 2016-04-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 87–455（369 aa） Fragment：UNP residues 87-455	Not recorded	MN MANGANESE (II) ION × 2 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 6KP 7-fluoro-4-(5-methyl-3H-imidazo[4,5-b]pyridin-6-yl)-2,4-dihydropyrazolo[4,3-b]indole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；40% MPD, 0.1M Hepes pH 7.0	Resolution 1.60 Å R-free 0.171
5JHU Potent, Reversible MetAP2 Inhibitors via FBDD Deposited 2016-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 87–455（369 aa） Fragment：UNP residues 87-455	Not recorded	MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 6KO [(2R)-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methyl 2-methoxybenzoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；277 K；30% MPD, 0.05M MES pH 5.9	Resolution 1.80 Å R-free 0.181
5JI6 Potent, Reversible MetAP2 Inhibitors via FBDD Deposited 2016-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 87–455（369 aa） Fragment：UNP residues 87-455	Not recorded	MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 1 6KN 4-(3-methylpyridin-4-yl)-6-(trifluoromethyl)-1H-indazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；24.% PEG MME 2000, 0.05M MES pH 5.9, 0.0175M Ammonium Sulfate	Resolution 2.15 Å R-free 0.230
5LYX CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 5-((R)-1-[1,2,4]Triazolo[1,5-a]pyrimidin-7-yl-pyrrolidin-2-ylmethoxy)-isoquinoline Deposited 2016-09-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa） Fragment：108-478	Mutation：none	7BF 5-[[(2~{R})-1-([1,2,4]triazolo[1,5-a]pyrimidin-7-yl)pyrrolidin-2-yl]methoxy]isoquinoline × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% methanol, 0.1 M citrate	Resolution 1.90 Å R-free 0.217
6QED CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-(2-oxo-1,2,3,4-tetrahydro-quinolin-6-yl)-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide Deposited 2019-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 HZK (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyrrolidine-3-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0	Resolution 1.80 Å R-free 0.198
6QEF CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-phenyl-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide Deposited 2019-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 HZW (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-phenyl-pyrrolidine-3-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0	Resolution 1.79 Å R-free 0.195
6QEG CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 2-Oxo-1-phenyl-pyrrolidine-3-carboxylic acid (2-thiophen-2-yl-ethyl)-amide Deposited 2019-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	GOL GLYCEROL × 1 K4K (3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0	Resolution 2.08 Å R-free 0.228
6QEH CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 5-Chloro-quinolin-8-ol Deposited 2019-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	GOL GLYCEROL × 1 HZQ 5-chloranylquinolin-8-ol × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0,	Resolution 2.17 Å R-free 0.220
6QEI CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 5,6-Difluoro-3-(2-isopropoxy-4-piperazin-1-yl-phenyl)-1H-indole-2-carboxylic acid amide Deposited 2019-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 HZE 5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0,	Resolution 1.80 Å R-free 0.209
6QEJ CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR Thiophene-2-sulfonic acid (4-fluoro-benzyl)-(4H-[1,2,4]triazol-3-ylmethyl)-amide Deposited 2019-01-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 HZT ~{N}-[(4-fluorophenyl)methyl]-~{N}-(1~{H}-1,2,4-triazol-5-ylmethyl)thiophene-2-sulfonamide × 1 TBU TERTIARY-BUTYL ALCOHOL × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；20% METHANOL, 0.1 M CITRATE, PH 6.0,	Resolution 1.62 Å R-free 0.184
7A12 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GW557358X (COMPOUND 9) Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	PO4 PHOSPHATE ION × 9 QVK 5-chloranyl-3-phenyl-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)	Resolution 2.00 Å R-free 0.198
7A13 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK1978537A (COMPOUND 27) Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	PO4 PHOSPHATE ION × 7 QW5 5-chloranyl-3-(3-methoxyphenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD).	Resolution 2.04 Å R-free 0.197
7A14 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2218325A (COMPOUND 32) Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	PO4 PHOSPHATE ION × 7 QVB 5-chloranyl-6-fluoranyl-3-(2-propan-2-yloxyphenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)	Resolution 2.14 Å R-free 0.215
7A15 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2224863A (COMPOUND 42) Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	PO4 PHOSPHATE ION × 7 QV5 5-chloranyl-6-fluoranyl-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)	Resolution 2.15 Å R-free 0.201
7A16 CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2229238A (COMPOUND 43) Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–478（371 aa）	Not recorded	PO4 PHOSPHATE ION × 7 HZE 5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)	Resolution 1.90 Å R-free 0.216
8ONY Human Methionine Aminopeptidase 2 at the 80S ribosome Deposited 2023-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–478（478 aa）	Not recorded	CO COBALT (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
8OXG Crystal structure of human methionine aminopeptidase-2 complexed with (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methyl-2-buten-1-yl)-2-oxiranyl]-1-oxaspiro[2.5]oct-6-yl N-(trans-4-aminocyclohexyl)carbamate Deposited 2023-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 108–478（371 aa） Chain B 108–478（371 aa）	Not recorded	W5N [(1~{R},2~{S},3~{S},4~{R})-2-methoxy-4-methyl-3-[(2~{R},3~{S})-2-methyl-3-(3-methylbut-2-enyl)oxiran-2-yl]-4-oxidanyl-cyclohexyl] ~{N}-(4-azanylcyclohexyl)carbamate × 2 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.73 Å R-free 0.215
9FPZ Human NatA-MAP2 80S ribosome complex Deposited 2024-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain A 1–478（478 aa）	Not recorded	CO COBALT (II) ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å

39 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–372； UniProt 108–478

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lyw
Deposition date deposition_date	2016-09-28
Structure title title	CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR 6-((R)-2-o-Tolyloxymethyl-pyrrolidin-1-yl)-9H-purine
Keywords keywords	HYDROLASE, PEPTIDASE, METAL ION BINDING, PROTEOLYSIS, HYDROLASE- HYDROLASE INHIBITOR COMPLEX; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.28 Å
Radius of gyration Rg (electron density) rg_electron	20.36 Å
Forward intensity I(0) i0	28965500.00
Molecular weight molecular_weight	40579.0 kDa
Excluded volume excluded_volume	50487 Å³
Envelope volume envelope_volume	58337 Å³
Hydration-shell volume shell_volume	23396 Å³
Envelope diameter envelope_diameter	71.1 Å
Shell Rg shell_rg	27.55 Å
Envelope Rg envelope_rg	20.93 Å
Shape Rg shape_rg	20.35 Å
Total Rg total_rg	21.29 Å
Total atoms total_atoms	2839
Residues n_residues	359
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.6 Å
Rg (real space) rg_real	21.16 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	2.8970e+07
I(0) uncertainty (real space) i0_real_error	3.3560e+05
Rg (reciprocal space) rg_reciprocal	21.18 Å
I(0) (reciprocal space) i0_reciprocal	28970000.0000
Solution quality estimate total_estimate	0.8983
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.187
Kurtosis Kurtosis kurtosis	-0.454
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10930000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Methionine aminopeptidase 2
Molecular weight formula_weight	42470.2 kDa
EC 编号 ec_number	3.4.11.18
Mutation mutation	none
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3095

MGPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDYHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine
Molecular weight formula_weight	309.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5lywA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	5lywA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	89.780 Å
Unit-cell length b length_b	100.230 Å
Unit-cell length c length_c	100.380 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	16.130 Å
R factor r_factor	0.1720
R_work r_work	0.1710
R_free r_free	0.1930

fit	/app/data/saxs_computation/ly/5lyw/5lyw.fit
pddf	/app/data/pr_computation/ly/5lyw/5lyw.pr.out
profile	/app/data/saxs_computation/ly/5lyw/5lyw.dat