[POCKETOME]
 

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28 entries [expand]
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AACL1_BRADU_2_326 [text] Amino acid--[acyl-carrier-protein] ligase 1 [Class-II aminoacyl-tRNA synthetase family. Amino acid--[acyl-carrier-protein] ligase subfamily]

volume: 736. Å3; shape: 0.35; buriedness: 0.79

negative: 0.09; positive: 0.17; polar: 0.16; backbone: 0.3; hydrophobic: 0.28

PDB: 3mey, 3mf1, 3mf2, 3pzc, 4h2s, 4h2t, 4h2u, 4h2v, 4h2w, 4h2x, 4h2y

HET: 5gp, amp, atp, coa, g5a, gap, h2v, mg, pns

EPMA_ECOLI_2_325 [text] Elongation factor P--(R)-beta-lysine ligase [Class-II aminoacyl-tRNA synthetase family. EpmA subfamily]

volume: 321. Å3; shape: 0.44; buriedness: 0.9

negative: 0.16; positive: 0.14; polar: 0.09; backbone: 0.4; hydrophobic: 0.21

Domains/regions: [R] Substrate binding

PDB: 3a5y, 3a5z, 3g1z

HET: amp, kaa

PYLS_METMA_185_454 [text] Pyrrolysine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 168. Å3; shape: 0.66; buriedness: 0.8

negative: 0.; positive: 0.15; polar: 0.; backbone: 0.13; hydrophobic: 0.72

PDB: 2e3c, 2q7e, 2q7g, 2q7h, 2zce, 2zim, 2zin, 2zio, 3qtc, 3vqv, 3vqw, 3vqx, 3vqy, 4bw9, 4bwa, 4ch3, 4ch4, 4ch5, 4ch6, 4cs2, 4cs3, 4cs4, 4q6g, 4tqd, 4tqf, 4zib, 5k1p, 5k1x

HET: axz

SYA_ECOLI_2_442 [text] Alanine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 375. Å3; shape: 0.72; buriedness: 0.96

negative: 0.19; positive: 0.23; polar: 0.05; backbone: 0.32; hydrophobic: 0.21

Domains/regions: [R] Catalytic

PDB: 3hxu, 3hxv, 3hxw, 3hxx, 3hxy, 3hxz, 3hy0, 3hy1

HET: 5al, a5a, acp, g5a, mdn, mg, ssa

SYA_PYRHO_1_752 [text] Alanine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 262. Å3; shape: 0.51; buriedness: 0.94

negative: 0.12; positive: 0.12; polar: 0.06; backbone: 0.42; hydrophobic: 0.29

PDB: 2zze, 2zzf, 2zzg

HET: a5a

SYFA_PSEAE_1_338 [text] Phenylalanine--tRNA ligase alpha subunit [Class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily]

volume: 321. Å3; shape: 0.58; buriedness: 0.88

negative: 0.05; positive: 0.; polar: 0.2; backbone: 0.39; hydrophobic: 0.37

PDB: 4p71, 4p72, 4p73, 4p74, 4p75

HET: 2nl, 2nm, 2u9, gax

SYFA_THET8_85_350 [text] Phenylalanine--tRNA ligase alpha subunit [Class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily]

volume: 382. Å3; shape: 0.38; buriedness: 0.92

negative: 0.09; positive: 0.1; polar: 0.1; backbone: 0.42; hydrophobic: 0.29

PDB: 1b70, 1b7y, 1eiy, 1jjc, 1pys, 2akw, 2aly, 2amc, 2iy5, 3hfz, 3teh, 4tva

HET: 200, dah, fa5, fya, mty, ysa

SYG_HUMAN_114_739 [text] Glycine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 588. Å3; shape: 0.74; buriedness: 0.8

negative: 0.22; positive: 0.15; polar: 0.04; backbone: 0.4; hydrophobic: 0.19

Domains/regions: [R] Substrate binding

PDB: 2pme, 2pmf, 2q5h, 2q5i, 2zt5, 2zt6, 2zt7, 2zt8, 2zxf, 4kqe, 4kr2, 4kr3, 4qei, 5e6m

HET: amp, anp, apc, atp, b4p, drv, gap

SYH_ECOLI_1_424 [text] Histidine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 374. Å3; shape: 0.41; buriedness: 0.94

negative: 0.11; positive: 0.14; polar: 0.24; backbone: 0.4; hydrophobic: 0.11

PDB: 1htt, 1kmm, 1kmn, 2el9

HET: amp, atp, ham, hso, hss

SYH_THET8_1_421 [text] Histidine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 355. Å3; shape: 0.39; buriedness: 0.94

negative: 0.1; positive: 0.1; polar: 0.23; backbone: 0.47; hydrophobic: 0.1

Domains/regions: [R] Catalytic

PDB: 1adj, 1ady, 1h4v, 4rdx

HET: amp, ham

SYK_GEOSE_2_494 [text] Lysine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 553. Å3; shape: 0.53; buriedness: 0.93

negative: 0.17; positive: 0.1; polar: 0.07; backbone: 0.47; hydrophobic: 0.2

PDB: 3a74, 3e9h, 3e9i

HET: b4p, kaa, lyn, mg, xah

SYK_HUMAN_69_581 [text] Lysine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 346. Å3; shape: 0.91; buriedness: 0.83

negative: 0.16; positive: 0.23; polar: 0.; backbone: 0.46; hydrophobic: 0.16

PDB: 3bju, 4dpg, 4ycu, 4ycw

HET: apc, atp, ca, krs, mg

SYP_ENTFA_1_572 [text] Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily]

volume: 313. Å3; shape: 0.56; buriedness: 0.92

negative: 0.18; positive: 0.16; polar: 0.09; backbone: 0.39; hydrophobic: 0.19

PDB: 2j3l, 2j3m

HET: atp, p5a, pri

SYP_METTH_2_472 [text] Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily]

volume: 294. Å3; shape: 0.51; buriedness: 0.95

negative: 0.13; positive: 0.17; polar: 0.19; backbone: 0.3; hydrophobic: 0.21

PDB: 1nj1, 1nj2, 1nj5, 1nj6

HET: 5ca, a5a, p5a

SYP_PLAF7_250_746 [text] Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily]

volume: 381. Å3; shape: 0.39; buriedness: 0.81

negative: 0.; positive: 0.05; polar: 0.25; backbone: 0.29; hydrophobic: 0.42

PDB: 4ncx, 4olf, 4q15, 4twa, 4wi1, 4ydq, 5ifu

HET: 3o6, gbm

SYP_RHOPA_2_438 [text] Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 2 subfamily]

volume: 339. Å3; shape: 0.57; buriedness: 0.92

negative: 0.16; positive: 0.09; polar: 0.15; backbone: 0.49; hydrophobic: 0.11

PDB: 2i4l, 2i4m, 2i4n, 2i4o

HET: 5ca, atp, mg, psd

SYP_THET8_1_477 [text] Proline--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily]

volume: 304. Å3; shape: 0.5; buriedness: 0.94

negative: 0.11; positive: 0.2; polar: 0.24; backbone: 0.33; hydrophobic: 0.12

PDB: 1h4q, 1h4s, 1h4t, 1hc7

HET: atp, pri, psd

SYS2_METBF_2_502 [text] Type-2 serine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily]

volume: 323. Å3; shape: 0.53; buriedness: 0.94

negative: 0.18; positive: 0.17; polar: 0.09; backbone: 0.28; hydrophobic: 0.27

Domains/regions: [R] Serine binding

PDB: 2cim, 2cj9, 2cja, 2cjb

HET: atp, ssa

SYSC_CANAL_1_462 [text] Serine--tRNA ligase, cytoplasmic [Class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily]

volume: 328. Å3; shape: 0.58; buriedness: 0.84

negative: 0.09; positive: 0.22; polar: 0.18; backbone: 0.37; hydrophobic: 0.14

Domains/regions: [R] Serine binding

PDB: 3qne, 3qo5, 3qo7, 3qo8

HET: atp, mg, ssa

SYSC_HUMAN_1_477 [text] Serine--tRNA ligase, cytoplasmic [Class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily]

volume: 273. Å3; shape: 0.47; buriedness: 0.92

negative: 0.15; positive: 0.14; polar: 0.22; backbone: 0.36; hydrophobic: 0.14

Domains/regions: [R] Serine binding

PDB: 3vbb, 4l87

HET: mg, ssa

SYS_PYRHO_1_455 [text] Serine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily]

volume: 255. Å3; shape: 0.56; buriedness: 0.87

negative: 0.22; positive: 0.16; polar: 0.21; backbone: 0.25; hydrophobic: 0.16

Domains/regions: [R] Serine binding

PDB: 2dq0, 2zr2, 2zr3

HET: amp, ssa

SYS_THET8_1_421 [text] Serine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily]

volume: 238. Å3; shape: 0.54; buriedness: 0.88

negative: 0.2; positive: 0.16; polar: 0.21; backbone: 0.27; hydrophobic: 0.16

Domains/regions: [R] Serine binding

PDB: 1ser, 1ses, 1set, 1sry

HET: ahx, amp, ssa

SYTC_HUMAN_320_723 [text] Threonine--tRNA ligase, cytoplasmic [Class-II aminoacyl-tRNA synthetase family]

volume: 558. Å3; shape: 0.58; buriedness: 0.76

negative: 0.15; positive: 0.22; polar: 0.22; backbone: 0.25; hydrophobic: 0.16

PDB: 4hwt, 4p3n, 4ttv

HET: 1b2, 2cr, bc9

SYT_ECOLI_1_239 [text] Threonine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 284. Å3; shape: 0.51; buriedness: 0.8

negative: 0.08; positive: 0.17; polar: 0.05; backbone: 0.39; hydrophobic: 0.32

PDB: 1qf6, 1tje, 1tke, 1tkg, 1tky

HET: a3s, ssa

SYT_ECOLI_239_642 [text] Threonine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 559. Å3; shape: 0.65; buriedness: 0.94

negative: 0.06; positive: 0.17; polar: 0.2; backbone: 0.33; hydrophobic: 0.24

Domains/regions: [R] Catalytic

PDB: 1evk, 1evl, 1fyf, 1kog, 1qf6, 4hwo, 4hwp, 4hwr, 4hws, 4p3o, 4p3p

HET: 1b2, 1b3, 2cr, 409, amp, ssa, tsb, x16

SYTM_YEAST_24_462 [text] Threonine--tRNA ligase, mitochondrial [Class-II aminoacyl-tRNA synthetase family]

volume: 301. Å3; shape: 0.51; buriedness: 0.95

negative: 0.09; positive: 0.19; polar: 0.27; backbone: 0.32; hydrophobic: 0.13

PDB: 3ugq, 3uh0, 4eo4, 4yye

HET: ssa, tsb

SYT_PYRAB_1_145 [text] Threonine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 290. Å3; shape: 0.86; buriedness: 0.89

negative: 0.; positive: 0.03; polar: 0.03; backbone: 0.51; hydrophobic: 0.43

PDB: 1y2q, 2hkz, 2hl0, 2hl1, 2hl2, 3pd2, 3pd3, 3pd4, 3pd5, 4rrq, 4rrr, 4s02, 4s03, 4s0i, 4s0j, 4s0k, 4s0l

HET: a3g, a3s, a3t, ssa, tsb

SYT_STAAW_1_645 [text] Threonine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

volume: 353. Å3; shape: 0.52; buriedness: 0.92

negative: 0.08; positive: 0.22; polar: 0.24; backbone: 0.22; hydrophobic: 0.24

Domains/regions: [R] Catalytic

PDB: 1nyq, 1nyr

HET: atp, tsb