2KODA

A high-resolution nmr structure of the dimeric c-terminal domain of hiv-1 ca
Total Genus 21
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
21
sequence length
88
structure length
88
Chain Sequence
MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL
Loading diagram...

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

publication title Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
pubmed doi rcsb
molecule tags Viral protein
source organism Hiv-1 m:b_hxb2r
molecule keywords HIV-1 CA C-terminal domain
total genus 21
structure length 88
sequence length 88
chains with identical sequence B
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2009-09-18
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A 2kodA00
3DS1A 2ONTA 2XXMA 3G1GA 5JPAA 4U0AA 1EOQA 3DS3A 4COPA 1A43A 2KODA 3G28A 5HGMA 4COCA 1AUMA 2JO0A 2XT1A 4PH0A 4XROA 3G26A 3H47A 3G29A 3DPHA 2JYGA 4U0CA 5I4TG 2BUOA 2M8PA 1E6JP 4PH1A 3G0VA 3DS5A 3MGEA 1BAJA 4QNBA 4XFZA 4IPYA 1D1DA 4U0DA 4WYMA 2L6EA 4XFXA 2LF4A 3DS0A 3G1IA 4U0BA 2M8LA 2M8NA 3G21A 4U0FA 3DS2A 5HGNA 2JYLA 1A8OA 4XFYA 3H4EA 5HGOA 3DTJA 4XRQA 3LRYA 1QRJA 3P05A 5DCKA 3VRLC 3DS4A 4M0IA 1EIAA 5HGLA 2XV6A 4U0EA 2EIAA 3NTEA
chains in the Genus database with same CATH superfamily
2K0DX 2VLPA 2QNWA 4DG9A 4U0AA 2KOPA 1GXGA 3EJBA 1VHNA 2WPTA 1AUMA 3EJEA 3H47A 2PEQA 3OW2O 3H0DA 1Q81Q 1Z6MA 4R0MA 2CGQA 5DCKA 4M0IA 2K0XA 1EIAA 2CG5B 3HYBA 2FHSC 1KQSO 1A43A 3EJDA 2JO0A 2L4BA 5F2NA 2GZFA 2KGAA 4U0BA 1BXIA 3DS2A 2PY8A 2LOLA 1GPJA 3LRYA 1QRJA 1QVGO 4GR6A 5BS1A 1ZNVA 2VLNA 3E2DA 3I55P 2BHVA 2N5IA 3G29A 1D1DA 2LKIA 3G0VA 3MGEA 2L22A 1M6NA 1VQ6P 4F37A 1ACPA 1K30A 2N50A 1N8RQ 2XZ0D 3P05A 1K8AQ 2KOSA 2ROQA 1NQ4A 1UNKA 2FQ2A 2MF4A 3CMAP 3CC7P 1VKUA 4XROA 3G26A 1DV5A 3DS5A 1YJNP 2LMLA 2K93A 2PEJA 1OR5A 1VQPP 2L0QA 2K0YA 2FADA 3G1GA 4COPA 2JBGA 1EMVA 5EW5E 2FVAA 2GZEA 1VQ7P 2M5RA 1K9MQ 1KC8Q 3CCVP 1Q7YQ 3CCUP 2VLQA 2FAEA 2K94A 2LTEA 1M6EX 2KW2A 1M1KQ 2KGDA 1EOQA 2AFDA 2FVEA 2XT1A 2PEKA 1VQKP 2KORA 4XFZA 3RG6C 5BS2A 4XFXA 2KG6A 2CNRA 2PENA 2JAZA 1HY8A 1VQ5P 1Q86Q 3G4SP 5JPAA 1DNYA 5KP6B 1AF8A 5HGMA 2BUOA 1YJWP 5KP7B 3G21A 2FQ1A 2LPKA 2KG8A 4XFYA 2E1MA 3CCLP 3DTJA 3DS4A 2FVFA 3Q20A 1Q82Q 1ZMBA 5HVCA 2OARA 2KODA 4NEOA 2Z44A 1KD1Q 1E0HA 2AVAA 2FQ0A 2MD9A 2K5XA 4IPYA 3WBHA 3HZQA 1GXHA 2M8NA 2VLOA 5HGNA 1L0IA 2Z45A 1L0HA 3M1MA 5F2OA 3VRLC 2EHTA 2XV6A 1YITP 2ONTA 1KLPA 3NY7B 4GR2A 2MY5A 1S72P 3GZMA 4CA3A 2L9FA 3B5IA 3U43A 2M8PA 1VQ8P 3CCRP 1M74A 2AF8A 4H2WC 2X2BA 2K2QA 2QA4P 2FACA 1VQ4P 4UHPB 2EFJA 2KGEA 3G71P 2LIWA 2AFEA 4PH0A 1YJ9P 3DPHA 1HQBA 4H2YC 3CPWO 3CC4P 1YI2P 4U0FA 4HKGA 1M90Q 1NJIQ 2MVUA 3GKLC 1X3OA 2XZ1C 2GZGA 4H2XC 1F80D 3GJNA 2N6ZA 2VSQA 1VQNP 4MRTC 4WYMA 2LF4A 3G1IA 5HV8A 2KR5A 2GDYA 2KOQA 2N98A 2K92A 5HGOA 2MVVA 3B4QA 4U0EA 2KWLA 1VQMP 2GDXA 2XXMA 1IMPA 2JGPA 2PEMA 4COCA 3CCMP 1BAJA 3DS0A 2JU1A 1K73Q 1AYIA 1YIJP 2MR7A 1T8KA 2EIAA 2ERHA 3NTEA 3DS3A 2CWOA 2JB0A 1VQOP 2DGYA 2N5HA 3CE7A 3G6EP 4PXHB 2KOOA 2JU2A 1IMQA 4BPFA 7CEIA 1A8OA 4PWVB 5EJDA 2PNGA 5KP8B 1W2BO 3I56P 2KGCA 2GYKA 3CCSP 2GZIA 2PEOA 4BPHA 2Z46A 5I4TG 1VQLP 4QNBA 4U0DA 2QEXP 1UJZA 2DNWA 3CCEP 2GZJA 3GZLA 3H4EA 4XRQA 2NO8A 3CCJP 4QKOA 2KG9A 5F2KA 2GDWA 2EG5A 2OTJP 1MZ8A 1YHQP 4U0CA 1E6JP 3CXCO 3CCQP 2LL8A 2CQ8A 1JJ2O 2JQ4A 1RO2A 1CEIA 1RO0A 3RG2A 4IZ6A 3DS1A 1VQ9P 2PEIA 2EHSA 2N6YA 3G28A 2OTLP 1QVFO 1IUQA 3CD6P 3LMOA 2JYGA 4PH1A 3CMEP 2L6EA 2M8LA 2P9XA 1RNIA 2JYLA 5CZDB 2LIUA 3CC2P 4BPGA 2MR8A 5HGLA 1FR2A
chains in the Genus database with same CATH topology
1YITP 2ONTA 3G1GA 4GR2A 4U0AA 3DS3A 4COPA 2CWOA 1S72P 1VQOP 1AUMA 2DGYA 3H47A 3B5IA 2M8PA 1VQ7P 1VQ8P 2PEQA 3CCRP 1M74A 3G6EP 3OW2O 3H0DA 1K9MQ 1KC8Q 3CCVP 1Q7YQ 3CCUP 1Q81Q 2QA4P 1A8OA 1M6EX 1VQ4P 5DCKA 4M0IA 1EIAA 2EFJA 3HYBA 1W2BO 3I56P 3G71P 1M1KQ 1KQSO 1EOQA 3CCSP 1A43A 2JO0A 4PH0A 2PEOA 2XT1A 5F2NA 1YJ9P 2PEKA 2Z46A 3DPHA 5I4TG 1VQKP 1VQLP 4XFZA 3RG6C 4QNBA 5BS2A 4U0DA 3CPWO 4XFXA 2QEXP 4U0BA 3CC4P 1YI2P 4U0FA 1M90Q 3DS2A 3CCEP 2PENA 2PY8A 3H4EA 1NJIQ 4XRQA 3LRYA 1QRJA 1QVGO 4GR6A 5BS1A 1VQ5P 1Q86Q 3CCJP 3G4SP 3E2DA 3I55P 5JPAA 2BHVA 5F2KA 2EG5A 2OTJP 5HGMA 1YHQP 3G29A 1VQNP 4U0CA 2BUOA 1E6JP 1D1DA 3G0VA 3MGEA 1YJWP 3CXCO 3CCQP 4WYMA 1M6NA 2LF4A 3G1IA 3G21A 1JJ2O 1VQ6P 1RO2A 4XFYA 1K30A 2E1MA 5HGOA 1RO0A 3DTJA 1N8RQ 3CCLP 1K8AQ 3P05A 3DS4A 4U0EA 3Q20A 1Q82Q 1VQMP 3DS1A 1VQ9P 2PEIA 2XXMA 1ZMBA 2OARA 2KODA 3G28A 3CMAP 2PEMA 2Z44A 3CC7P 4COCA 1KD1Q 2OTLP 1QVFO 1IUQA 3G26A 4XROA 3CD6P 3CCMP 2JYGA 4PH1A 3DS5A 1BAJA 1YJNP 4IPYA 3CMEP 2L6EA 3WBHA 2M8LA 3DS0A 2P9XA 3HZQA 2M8NA 1RNIA 1K73Q 5HGNA 2JYLA 2PEJA 2Z45A 1YIJP 1VQPP 3M1MA 5F2OA 3CC2P 3VRLC 5HGLA 2XV6A 2EIAA 3NTEA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3DS1 A;  2ONT A;  2XXM A;  3G1G A;  5JPA A;  4U0A A;  1EOQ A;  3DS3 A;  4COP A;  1A43 A;  2KOD A;  3G28 A;  5HGM A;  4COC A;  1AUM A;  2JO0 A;  2XT1 A;  4PH0 A;  4XRO A;  3G26 A;  3H47 A;  3G29 A;  3DPH A;  2JYG A;  4U0C A;  5I4T G;  2BUO A;  2M8P A;  1E6J P;  4PH1 A;  3G0V A;  3DS5 A;  3MGE A;  1BAJ A;  4QNB A;  4XFZ A;  4IPY A;  1D1D A;  4U0D A;  4WYM A;  2L6E A;  4XFX A;  2LF4 A;  3DS0 A;  3G1I A;  4U0B A;  2M8L A;  2M8N A;  3G21 A;  4U0F A;  3DS2 A;  5HGN A;  2JYL A;  1A8O A;  4XFY A;  3H4E A;  5HGO A;  3DTJ A;  4XRQ A;  3LRY A;  1QRJ A;  3P05 A;  5DCK A;  3VRL C;  3DS4 A;  4M0I A;  1EIA A;  5HGL A;  2XV6 A;  4U0E A;  2EIA A;  3NTE A; 
#chains in the Genus database with same CATH topology
 2K0D X;  2VLP A;  2QNW A;  4DG9 A;  4U0A A;  2KOP A;  1GXG A;  3EJB A;  1VHN A;  2WPT A;  1AUM A;  3EJE A;  3H47 A;  2PEQ A;  3OW2 O;  3H0D A;  1Q81 Q;  1Z6M A;  4R0M A;  2CGQ A;  5DCK A;  4M0I A;  2K0X A;  1EIA A;  2CG5 B;  3HYB A;  2FHS C;  1KQS O;  1A43 A;  3EJD A;  2JO0 A;  2L4B A;  5F2N A;  2GZF A;  2KGA A;  4U0B A;  1BXI A;  3DS2 A;  2PY8 A;  2LOL A;  1GPJ A;  3LRY A;  1QRJ A;  1QVG O;  4GR6 A;  5BS1 A;  1ZNV A;  2VLN A;  3E2D A;  3I55 P;  2BHV A;  2N5I A;  3G29 A;  1D1D A;  2LKI A;  3G0V A;  3MGE A;  2L22 A;  1M6N A;  1VQ6 P;  4F37 A;  1ACP A;  1K30 A;  2N50 A;  1N8R Q;  2XZ0 D;  3P05 A;  1K8A Q;  2KOS A;  2ROQ A;  1NQ4 A;  1UNK A;  2FQ2 A;  2MF4 A;  3CMA P;  3CC7 P;  1VKU A;  4XRO A;  3G26 A;  1DV5 A;  3DS5 A;  1YJN P;  2LML A;  2K93 A;  2PEJ A;  1OR5 A;  1VQP P;  2L0Q A;  2K0Y A;  2FAD A;  3G1G A;  4COP A;  2JBG A;  1EMV A;  5EW5 E;  2FVA A;  2GZE A;  1VQ7 P;  2M5R A;  1K9M Q;  1KC8 Q;  3CCV P;  1Q7Y Q;  3CCU P;  2VLQ A;  2FAE A;  2K94 A;  2LTE A;  1M6E X;  2KW2 A;  1M1K Q;  2KGD A;  1EOQ A;  2AFD A;  2FVE A;  2XT1 A;  2PEK A;  1VQK P;  2KOR A;  4XFZ A;  3RG6 C;  5BS2 A;  4XFX A;  2KG6 A;  2CNR A;  2PEN A;  2JAZ A;  1HY8 A;  1VQ5 P;  1Q86 Q;  3G4S P;  5JPA A;  1DNY A;  5KP6 B;  1AF8 A;  5HGM A;  2BUO A;  1YJW P;  5KP7 B;  3G21 A;  2FQ1 A;  2LPK A;  2KG8 A;  4XFY A;  2E1M A;  3CCL P;  3DTJ A;  3DS4 A;  2FVF A;  3Q20 A;  1Q82 Q;  1ZMB A;  5HVC A;  2OAR A;  2KOD A;  4NEO A;  2Z44 A;  1KD1 Q;  1E0H A;  2AVA A;  2FQ0 A;  2MD9 A;  2K5X A;  4IPY A;  3WBH A;  3HZQ A;  1GXH A;  2M8N A;  2VLO A;  5HGN A;  1L0I A;  2Z45 A;  1L0H A;  3M1M A;  5F2O A;  3VRL C;  2EHT A;  2XV6 A;  1YIT P;  2ONT A;  1KLP A;  3NY7 B;  4GR2 A;  2MY5 A;  1S72 P;  3GZM A;  4CA3 A;  2L9F A;  3B5I A;  3U43 A;  2M8P A;  1VQ8 P;  3CCR P;  1M74 A;  2AF8 A;  4H2W C;  2X2B A;  2K2Q A;  2QA4 P;  2FAC A;  1VQ4 P;  4UHP B;  2EFJ A;  2KGE A;  3G71 P;  2LIW A;  2AFE A;  4PH0 A;  1YJ9 P;  3DPH A;  1HQB A;  4H2Y C;  3CPW O;  3CC4 P;  1YI2 P;  4U0F A;  4HKG A;  1M90 Q;  1NJI Q;  2MVU A;  3GKL C;  1X3O A;  2XZ1 C;  2GZG A;  4H2X C;  1F80 D;  3GJN A;  2N6Z A;  2VSQ A;  1VQN P;  4MRT C;  4WYM A;  2LF4 A;  3G1I A;  5HV8 A;  2KR5 A;  2GDY A;  2KOQ A;  2N98 A;  2K92 A;  5HGO A;  2MVV A;  3B4Q A;  4U0E A;  2KWL A;  1VQM P;  2GDX A;  2XXM A;  1IMP A;  2JGP A;  2PEM A;  4COC A;  3CCM P;  1BAJ A;  3DS0 A;  2JU1 A;  1K73 Q;  1AYI A;  1YIJ P;  2MR7 A;  1T8K A;  2EIA A;  2ERH A;  3NTE A;  3DS3 A;  2CWO A;  2JB0 A;  1VQO P;  2DGY A;  2N5H A;  3CE7 A;  3G6E P;  4PXH B;  2KOO A;  2JU2 A;  1IMQ A;  4BPF A;  7CEI A;  1A8O A;  4PWV B;  5EJD A;  2PNG A;  5KP8 B;  1W2B O;  3I56 P;  2KGC A;  2GYK A;  3CCS P;  2GZI A;  2PEO A;  4BPH A;  2Z46 A;  5I4T G;  1VQL P;  4QNB A;  4U0D A;  2QEX P;  1UJZ A;  2DNW A;  3CCE P;  2GZJ A;  3GZL A;  3H4E A;  4XRQ A;  2NO8 A;  3CCJ P;  4QKO A;  2KG9 A;  5F2K A;  2GDW A;  2EG5 A;  2OTJ P;  1MZ8 A;  1YHQ P;  4U0C A;  1E6J P;  3CXC O;  3CCQ P;  2LL8 A;  2CQ8 A;  1JJ2 O;  2JQ4 A;  1RO2 A;  1CEI A;  1RO0 A;  3RG2 A;  4IZ6 A;  3DS1 A;  1VQ9 P;  2PEI A;  2EHS A;  2N6Y A;  3G28 A;  2OTL P;  1QVF O;  1IUQ A;  3CD6 P;  3LMO A;  2JYG A;  4PH1 A;  3CME P;  2L6E A;  2M8L A;  2P9X A;  1RNI A;  2JYL A;  5CZD B;  2LIU A;  3CC2 P;  4BPG A;  2MR8 A;  5HGL A;  1FR2 A; 
#chains in the Genus database with same CATH homology
 1YIT P;  2ONT A;  3G1G A;  4GR2 A;  4U0A A;  3DS3 A;  4COP A;  2CWO A;  1S72 P;  1VQO P;  1AUM A;  2DGY A;  3H47 A;  3B5I A;  2M8P A;  1VQ7 P;  1VQ8 P;  2PEQ A;  3CCR P;  1M74 A;  3G6E P;  3OW2 O;  3H0D A;  1K9M Q;  1KC8 Q;  3CCV P;  1Q7Y Q;  3CCU P;  1Q81 Q;  2QA4 P;  1A8O A;  1M6E X;  1VQ4 P;  5DCK A;  4M0I A;  1EIA A;  2EFJ A;  3HYB A;  1W2B O;  3I56 P;  3G71 P;  1M1K Q;  1KQS O;  1EOQ A;  3CCS P;  1A43 A;  2JO0 A;  4PH0 A;  2PEO A;  2XT1 A;  5F2N A;  1YJ9 P;  2PEK A;  2Z46 A;  3DPH A;  5I4T G;  1VQK P;  1VQL P;  4XFZ A;  3RG6 C;  4QNB A;  5BS2 A;  4U0D A;  3CPW O;  4XFX A;  2QEX P;  4U0B A;  3CC4 P;  1YI2 P;  4U0F A;  1M90 Q;  3DS2 A;  3CCE P;  2PEN A;  2PY8 A;  3H4E A;  1NJI Q;  4XRQ A;  3LRY A;  1QRJ A;  1QVG O;  4GR6 A;  5BS1 A;  1VQ5 P;  1Q86 Q;  3CCJ P;  3G4S P;  3E2D A;  3I55 P;  5JPA A;  2BHV A;  5F2K A;  2EG5 A;  2OTJ P;  5HGM A;  1YHQ P;  3G29 A;  1VQN P;  4U0C A;  2BUO A;  1E6J P;  1D1D A;  3G0V A;  3MGE A;  1YJW P;  3CXC O;  3CCQ P;  4WYM A;  1M6N A;  2LF4 A;  3G1I A;  3G21 A;  1JJ2 O;  1VQ6 P;  1RO2 A;  4XFY A;  1K30 A;  2E1M A;  5HGO A;  1RO0 A;  3DTJ A;  1N8R Q;  3CCL P;  1K8A Q;  3P05 A;  3DS4 A;  4U0E A;  3Q20 A;  1Q82 Q;  1VQM P;  3DS1 A;  1VQ9 P;  2PEI A;  2XXM A;  1ZMB A;  2OAR A;  2KOD A;  3G28 A;  3CMA P;  2PEM A;  2Z44 A;  3CC7 P;  4COC A;  1KD1 Q;  2OTL P;  1QVF O;  1IUQ A;  3G26 A;  4XRO A;  3CD6 P;  3CCM P;  2JYG A;  4PH1 A;  3DS5 A;  1BAJ A;  1YJN P;  4IPY A;  3CME P;  2L6E A;  3WBH A;  2M8L A;  3DS0 A;  2P9X A;  3HZQ A;  2M8N A;  1RNI A;  1K73 Q;  5HGN A;  2JYL A;  2PEJ A;  2Z45 A;  1YIJ P;  1VQP P;  3M1M A;  5F2O A;  3CC2 P;  3VRL C;  5HGL A;  2XV6 A;  2EIA A;  3NTE A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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